Research workbench

E. COLI methionine aminopeptidase in complex with thiabendazole

Analyse E. COLI methionine aminopeptidase in complex with thiabendazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YVM
Type: protein
Length: 262 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionine aminopeptidase
EC: 3.4.11.18
UniProt: P07906
Ligands: TMG, CO, NA
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionine aminopeptidase (EC 3.4.11.18)	protein	262	28% helix, 29% strand	P07906

Ligands and binding sites

TMG · 2-(1,3-thiazol-4-yl)-1H-benzimidazole · ligand · chains A
CO · Cobalt (II) ion · metal · 4 copies · chains A
NA · Sodium ion · metal · chains A

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

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	157	0.57	0.82	29	CO, TMG
2	68	0.28	0.73	13	empty

Compared structures

1YVM · E. coli Methionine Aminopeptidase in complex with thiabendazole · 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 P07906
Elsewhere: RCSB PDB 1YVM · PDBe 1YVM · UniProt P07906

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