3LQI

Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Bromodomain	e3lqiA1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)
A	PHD	e3lqiA2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (1.6)
B	Bromodomain	e3lqiB1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)
B	PHD	e3lqiB2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (1.6)
C	Bromodomain	e3lqiC1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)
C	PHD	e3lqiC2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	MLL1 PHD3-Bromo	sequence-specific DNA binding DNA binding binding unmethylated CpG binding nucleic acid binding protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K4 methyltransferase activity lysine N-methyltransferase activity sequence-specific DNA binding DNA binding binding unmethylated CpG binding nucleic acid binding protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K4 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity histone H3K4 trimethyltransferase activity S-methyltransferase activity protein-cysteine methyltransferase activity histone H3K4 monomethyltransferase activity DNA secondary structure binding minor groove of adenine-thymine-rich DNA binding identical protein binding protein binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein binding chromatin binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process behavior multicellular organismal process exploration behavior macromolecule modification protein metabolic process protein modification process multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells methylation apoptotic process cell death programmed cell death response to stimulus response to potassium ion response to metal ion response to chemical rhythmic process circadian regulation of gene expression circadian rhythm developmental process cellular developmental process hemopoiesis animal organ development cell development embryo development multicellular organism development embryonic hemopoiesis cell differentiation anatomical structure development embryonic organ development immune system development spleen development immune system process hematopoietic or lymphoid organ development system development fibroblast proliferation cell population proliferation negative regulation of cell population proliferation negative regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of fibroblast proliferation definitive hemopoiesis positive regulation of DNA-templated transcription regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular response to endogenous stimulus cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor response to light stimulus system process learning learning or memory nervous system process visual learning visual behavior cognition associative learning response to radiation response to abiotic stimulus regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling regulation of short-term neuronal synaptic plasticity regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of biological quality mononuclear cell differentiation lymphocyte activation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation involved in immune response alpha-beta T cell differentiation involved in immune response leukocyte activation alpha-beta T cell differentiation type 2 immune response T cell activation involved in immune response alpha-beta T cell activation involved in immune response T cell activation CD4-positive, alpha-beta T cell activation leukocyte activation involved in immune response alpha-beta T cell activation T-helper 2 cell differentiation T cell differentiation lymphocyte activation involved in immune response immune response T-helper cell differentiation cell activation T cell differentiation involved in immune response immune effector process leukocyte differentiation membrane depolarization regulation of membrane potential post-embryonic development anterior/posterior pattern specification pattern specification process regionalization regulation of cellular component organization negative regulation of DNA methylation-dependent heterochromatin formation negative regulation of heterochromatin formation negative regulation of chromatin organization negative regulation of macromolecule metabolic process regulation of heterochromatin formation regulation of chromatin organization heterochromatin formation negative regulation of cellular component organization negative regulation of metabolic process negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic	membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm membrane-bounded organelle protein-containing complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen cytoplasm cytosol MLL1/2 complex MLL1 complex
D [auth R], E [auth S], F [auth T]	Histone H3	DNA binding binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization biosynthetic process protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR001965	Zinc finger, PHD-type	Domain
A, B, C	IPR046341	SET domain superfamily	Homologous Superfamily
A, B, C	IPR001214	SET domain	Domain
A, B, C	IPR044133	KMT2A, PHD domain 3	Domain
A, B, C	IPR003616	Post-SET domain	Domain
A, B, C	IPR034732	Extended PHD (ePHD) domain	Domain
A, B, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A, B, C	IPR003888	FY-rich, N-terminal	Conserved Site
A, B, C	IPR001487	Bromodomain	Domain
A, B, C	IPR002857	Zinc finger, CXXC-type	Domain
A, B, C	IPR019787	Zinc finger, PHD-finger	Domain
A, B, C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, C	IPR041958	KMT2A, ePHD domain	Domain
A, B, C	IPR047219	Histone-lysine N-methyltransferase 2A/2B, SET domain	Domain
A, B, C	IPR042025	KMT2A, PHD domain 2	Domain
A, B, C	IPR003889	FY-rich, C-terminal	Conserved Site
A, B, C	IPR016569	Methyltransferase, trithorax	Family
A, B, C	IPR042023	KMT2A, PHD domain 1	Domain
D [auth R], E [auth S], F [auth T]	IPR009072	Histone-fold	Homologous Superfamily
D [auth R], E [auth S], F [auth T]	IPR007125	Histone H2A/H2B/H3	Domain
D [auth R], E [auth S], F [auth T]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q03164	myeloid leukemia acute myeloid leukemia acute monocytic leukemia Wiedemann-Steiner syndrome transitional cell carcinoma urinary bladder cancer cancer Chromosome Aberrations acute biphenotypic leukemia adenocarcinoma leukemia chronic monocytic leukemia acute myelomonocytic leukemia M4 tubular adenocarcinoma prostate cancer myeloid leukemia acute myeloid leukemia acute monocytic leukemia Wiedemann-Steiner syndrome transitional cell carcinoma urinary bladder cancer cancer Chromosome Aberrations acute biphenotypic leukemia adenocarcinoma leukemia chronic monocytic leukemia acute myelomonocytic leukemia M4 tubular adenocarcinoma prostate cancer granular cell carcinoma small cell lung carcinoma lymphoid leukemia osteosarcoma Pick disease Cornelia de Lange syndrome cribriform carcinoma of breast gastric neoplasm small cell carcinoma spina bifida hereditary diffuse gastric adenocarcinoma tuberculosis urinary bladder neoplasm Alzheimer disease malignant ependymoma medulloblastoma breast cancer celiac disease ovarian cancer Cornelia de Lange syndrome 1 primitive neuroectodermal tumor psoriasis acute lymphoblastic leukemia glioblastoma hematologic disease subependymal giant cell astrocytoma intellectual disability astrocytic tumor malignant mesothelioma bilineal acute myeloid leukemia metabolic syndrome X Burkitt lymphoma oligodendroglioma childhood acute lymphoblastic leukemia pancreatic ductal adenocarcinoma congenital anemia cribriform carcinoma gastric cancer schizophrenia hepatocellular carcinoma acute undifferentiated leukemia large cell medulloblastoma X-linked mixed deafness with perilymphatic gusher atypical teratoid rhabdoid tumor brain glioma
D [auth R], E [auth S], F [auth T]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth R], E [auth S], F [auth T]	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084