MolNFT v1 · #118544 · protein

Structure of E.COLI glpg complexed with peptidic inhibitor ac-vrma-cho

5F5B · Rhomboid protease glpg: “Structure of E.COLI glpg complexed with peptidic inhibitor ac-vrma-cho”. X-ray diffraction, 1 ligand (ACE), 1 pocket (best druggability 0.36). MolNFT v1 #118544 on GenesisL1: 3D structure, binding sites and…

PDB: 5F5B
Type: protein
Length: 186 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhomboid protease glpg; Peptidic derivative of gurken: ACE-val-arg-met-ala- aldehyde
EC: 3.4.21.105
UniProt: A0A0J2E248
Ligands: ACE
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 2 distinct chains · 73% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhomboid protease glpg (EC 3.4.21.105)	protein	182	74% helix, 2% strand	A0A0J2E248
B	Peptidic derivative of gurken: ACE-val-arg-met-ala- aldehyde	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	84	0.36	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 481 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).

Compared structures

5F5B · Structure of E.Coli GlpG complexed with peptidic inhibitor Ac-VRMA-CHO · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A0J2E248
Elsewhere: RCSB PDB 5F5B · PDBe 5F5B · UniProt A0A0J2E248

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