6VJ9 | pdb_00006vj9

Crystal structure of GlpG in complex with peptide boronate inhibitor

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Rhomboid-like	8038801	3000368	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	Rhomboid	e6vj9A1	A: alpha bundles	X: Rhomboid-like (From Topology)	H: Rhomboid-like (From Topology)	T: Rhomboid-like	F: Rhomboid	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01694	Rhomboid domain (Rhomboid)	Rhomboid domain	This domain is found in a family of integral membrane proteins that are related to Drosophila rhomboid protein Swiss:P20350. Members of this family are mainly found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored T ...	This domain is found in a family of integral membrane proteins that are related to Drosophila rhomboid protein Swiss:P20350. Members of this family are mainly found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease [2,3,4] (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite [5]. This domain shows six transmembrane helices.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	ACE-VAL-ARG-MET-B2A	-	-	-
A	Rhomboid family intramembrane serine protease GlpG	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	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR022732	Peptidase S54, GlpG peptidase, N-terminal	Domain
A	IPR038236	GlpG peptidase, N-terminal domain superfamily	Homologous Superfamily
A	IPR022764	Peptidase S54, rhomboid domain	Domain
A	IPR023662	Rhomboid protease GlpG	Family
A	IPR035952	Rhomboid-like superfamily	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A	MemProtMD	Annotated as membrane protein by MemProtMD

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359
B	B2A	Parent Component: ALA RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354

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.