4GGQ | pdb_00004ggq

Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with CJ40

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rotamase-like	8065266	3000622	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Rotamase-like	8065266	3000622	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Rotamase-like	8065266	3000622	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Rotamase-like	8065266	3000622	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Ubiquitin-like	8034468	3000157	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	GFO_IDH_MocA	e4ggqD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: GFO_IDH_MocA	ECOD (v294.1)
D	DNA_gyraseB_C,Toprim	e4ggqD3	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)
C [auth B]	GFO_IDH_MocA	e4ggqB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: GFO_IDH_MocA	ECOD (v294.1)
C [auth B]	DNA_gyraseB_C,Toprim	e4ggqB2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DNA_gyraseB_C,Toprim	ECOD (v294.1)
B [auth A]	GFO_IDH_MocA	e4ggqA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: GFO_IDH_MocA	ECOD (v294.1)
B [auth A]	CHORD	e4ggqA2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: CHORD	ECOD (v294.1)
A [auth C]	GFO_IDH_MocA	e4ggqC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: GFO_IDH_MocA	ECOD (v294.1)
A [auth C]	CHORD	e4ggqC2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: CHORD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.50.40	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)
C [auth B]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C [auth B]	3.10.50.40	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)
B [auth A]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B [auth A]	3.10.50.40	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)
A [auth C]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A [auth C]	3.10.50.40	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth A], C [auth B], D	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth A], C [auth B], D	Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase	protein tag activity molecular tag activity protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity cation binding ion binding protein tag activity molecular tag activity protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity cation binding ion binding metal ion binding small molecule binding	peptidyl-lysine modification primary metabolic process protein sumoylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal	intracellular anatomical structure cell cortex septin ring intracellular membraneless organelle intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle septin cytoskeleton cytoplasm membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure cell cortex septin ring intracellular membraneless organelle intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle septin cytoskeleton cytoplasm membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth A], C [auth B], D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A [auth C], B [auth A], C [auth B], D	IPR000626	Ubiquitin-like domain	Domain
A [auth C], B [auth A], C [auth B], D	IPR022617	Rad60/SUMO-like domain	Domain
A [auth C], B [auth A], C [auth B], D	IPR046357	Peptidyl-prolyl cis-trans isomerase domain superfamily	Homologous Superfamily
A [auth C], B [auth A], C [auth B], D	IPR001179	FKBP-type peptidyl-prolyl cis-trans isomerase domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.