4A8B | pdb_00004a8b

Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozymes

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Trypsin-like serine proteases	8073980	3000114	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Lysozyme-like	8037428	3001879	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)
A	RNA_pol_Rpb1_3	e4a8bA3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
A	Aminotran_3	e4a8bA2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
B	RNA_pol_Rpb1_3	e4a8bB3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
B	Aminotran_3	e4a8bB2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
C	RNA_pol_Rpb1_3	e4a8bC3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
C	Aminotran_3	e4a8bC2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
D	RNA_pol_Rpb1_3	e4a8bD3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
D	Aminotran_3	e4a8bD2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
E	RNA_pol_Rpb1_3	e4a8bE3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
E	Aminotran_3	e4a8bE2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
G	RNA_pol_Rpb1_3	e4a8bG3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
G	Aminotran_3	e4a8bG2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
H	RNA_pol_Rpb1_3	e4a8bH3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
H	Aminotran_3	e4a8bH2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
J	RNA_pol_Rpb1_3	e4a8bJ3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
J	Aminotran_3	e4a8bJ2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
K	RNA_pol_Rpb1_3	e4a8bK3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
K	Aminotran_3	e4a8bK2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
L	RNA_pol_Rpb1_3	e4a8bL3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
L	Aminotran_3	e4a8bL2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
I	RNA_pol_Rpb1_3	e4a8bI3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
I	Aminotran_3	e4a8bI2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
F	RNA_pol_Rpb1_3	e4a8bF3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: RNA_pol_Rpb1_3	ECOD (v294.1)
F	Aminotran_3	e4a8bF2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Aminotran_3	ECOD (v294.1)
M	RRM_1	e4a8bM1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
N	RRM_1	e4a8bN1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
O	RRM_1	e4a8bO1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
P	RRM_1	e4a8bP1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
Q	RRM_1	e4a8bQ1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
R	RRM_1	e4a8bR1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF13365	Trypsin-like peptidase domain (Trypsin_2)	Trypsin-like peptidase domain	This family includes trypsin-like peptidase domains.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain
M, N, O, P, Q M, N, O, P, Q, R	PF00062	C-type lysozyme/alpha-lactalbumin family (Lys)	C-type lysozyme/alpha-lactalbumin family	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bac ...	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity identical protein binding protein binding binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process catabolic process protein catabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process	cellular anatomical structure extracellular region periplasmic space
M, N, O, P, Q M, N, O, P, Q, R	LYSOZYME C	hydrolase activity, acting on glycosyl bonds hexosaminidase activity beta-N-acetylhexosaminidase activity beta-N-acetylglucosaminidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity peptidoglycan muralytic activity lysozyme activity identical protein binding protein binding binding	catabolic process cell wall organization or biogenesis metabolic process cellular process macromolecule metabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing response to stimulus catabolic process cell wall organization or biogenesis metabolic process cellular process macromolecule metabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing response to stimulus response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium response to bacterium response to stress response to external biotic stimulus defense response to Gram-positive bacterium	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR011782	Peptidase S1C, Do	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR001478	PDZ domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR001940	Peptidase S1C	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR036034	PDZ superfamily	Homologous Superfamily
M, N, O, P, Q M, N, O, P, Q, R	IPR001916	Glycoside hydrolase, family 22	Family
M, N, O, P, Q M, N, O, P, Q, R	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
M, N, O, P, Q M, N, O, P, Q, R	IPR019799	Glycoside hydrolase family 22 domain	Domain
M, N, O, P, Q M, N, O, P, Q, R	IPR000974	Glycoside hydrolase, family 22, lysozyme	Family