3OTP | pdb_00003otp

Crystal structure of the DegP dodecamer with a model substrate

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)
F	SCOP2B Superfamily	Trypsin-like serine proteases	8040753	3000114	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PDZ domain-like	8040752	3000388	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PDZ domain-like	8040752	3000388	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Trypsin-like serine proteases	8040753	3000114	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trypsin-like serine proteases	8040753	3000114	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PDZ domain-like	8040752	3000388	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PDZ domain-like	8040752	3000388	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8040753	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8040753	3000114	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PDZ domain-like	8040752	3000388	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PDZ domain-like	8040752	3000388	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8040753	3000114	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)
G		e3otpG01	A: a/b three-layered sandwiches	X: Rossmann-like	H: P-loop domains-related	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F:	ECOD (v294.1)
F	Gal-bind_lectin	e3otpF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)
F	SidM_Rab1-act	e3otpF6	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: SidM_Rab1-act	ECOD (v294.1)
E	V-set	e3otpE10	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (v294.1)
D	V-set	e3otpD10	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (v294.1)
C	Gal-bind_lectin	e3otpC2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)
C	SidM_Rab1-act	e3otpC6	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: SidM_Rab1-act	ECOD (v294.1)
B	V-set	e3otpB10	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (v294.1)
A	FKBP_C	e3otpA1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: Macro domain-like	T: Macro domain-like	F: FKBP_C	ECOD (v294.1)
A	SidM_Rab1-act	e3otpA5	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: SidM_Rab1-act	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.40.10.120	Mainly Beta	Beta Barrel	Thrombin, subunit H		CATH (4.3.0)
F	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
E	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
E	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
D	2.40.10.120	Mainly Beta	Beta Barrel	Thrombin, subunit H		CATH (4.3.0)
D	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
C	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
C	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
B	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
A	2.40.10.120	Mainly Beta	Beta Barrel	Thrombin, subunit H		CATH (4.3.0)
A	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, J, K G, H, I, J, K, L	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 extracellular region extracellular space membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system
A, B, C, D, E A, B, C, D, E, F	Protease do	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein binding binding	protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation response to oxidative stress response to stimulus response to stress proteolysis protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation response to oxidative stress response to stimulus response to stress proteolysis response to heat response to abiotic stimulus response to temperature stimulus catabolic process protein catabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process	cell periphery cellular anatomical structure plasma membrane membrane periplasmic space outer membrane-bounded periplasmic space cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

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