3GCD | pdb_00003gcd

Structure of the V. cholerae RTX cysteine protease domain in complex with an aza-Leucine peptide inhibitor

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	Caspase-like	8104068	3001096	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Caspase-like	8104068	3001096	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Caspase-like	8104068	3001096	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Caspase-like	8104068	3001096	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	Ras	e3gcdD1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Ras	ECOD (develop294)
C	Ras	e3gcdC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Ras	ECOD (develop294)
B	Ras	e3gcdB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Ras	ECOD (develop294)
A	Indigoidine_A	e3gcdA1	A: alpha bundles	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Indigoidine_A	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.11050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	MARTX cysteine protease (CPD) domain	CATH (4.3.0)
C	3.40.50.11050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	MARTX cysteine protease (CPD) domain	CATH (4.3.0)
B	3.40.50.11050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	MARTX cysteine protease (CPD) domain	CATH (4.3.0)
A	3.40.50.11050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	MARTX cysteine protease (CPD) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF11713	Peptidase C80 family (Peptidase_C80)	Peptidase C80 family	This family belongs to cysteine peptidase family C80.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RTX toxin RtxA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding peptidyl-lysine N6-palmitoyltransferase activity catalytic activity, acting on a protein acyltransferase activity CoA-dependent peptidyl-lysine N6-palmitoyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity N-acyltransferase activity lipid binding toxin activity ligase activity cysteine-type peptidase activity peptidase activity hydrolase activity cation binding metal ion binding	cellular component organization organelle organization actin cytoskeleton organization actin filament organization actin filament-based process cellular process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region host cell cytosol host cell cytoplasm part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000073	Alpha/beta hydrolase fold-1	Domain
A, B, C, D	IPR038383	CGT/MARTX, cysteine protease (CPD) domain superfamily	Homologous Superfamily
A, B, C, D	IPR032074	Actin cross-linking domain	Domain
A, B, C, D	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily
A, B, C, D	IPR011509	RtxA toxin	Repeat
A, B, C, D	IPR020974	CGT/MARTX, cysteine protease (CPD) domain	Domain
A, B, C, D	IPR049824	RtxA toxin-like, peptidase C80 cysteine binding domain	Domain
A, B, C, D	IPR020972	Dermonecrotic/RTX toxin, membrane localization domain	Domain
A, B, C, D	IPR048568	RTX toxin, C-terminal repeat	Repeat
A, B, C, D	IPR011049	Serralysin-like metalloprotease, C-terminal	Homologous Superfamily

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.