MolNFT v1 · #25991 · protein

Znmg substituted aminopeptidase P from E. COLI

1WBQ · Xaa-pro aminopeptidase: “Znmg substituted aminopeptidase P from E. COLI”. X-ray diffraction, 3 ligands (MG, ZN, CL), 13 pockets (best druggability 0.86). MolNFT v1 #25991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1WBQ
Type: protein
Length: 1,757 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xaa-pro aminopeptidase
EC: 3.4.11.9
UniProt: P15034
Ligands: MG, ZN, CL
Pockets: 13 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xaa-pro aminopeptidase (EC 3.4.11.9)	protein	440	41% helix, 19% strand	P15034
B, C, D	Xaa-pro aminopeptidase (EC 3.4.11.9)	protein	439	41% helix, 19% strand	P15034

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	809	0.86	0.89	101	empty
2	956	0.76	0.79	77	empty
3	220	0.71	0.87	35	empty
4	611	0.65	0.76	74	empty
5	594	0.64	0.75	67	empty

Interfaces

3 interfaces between chains.

A–B · 2163 Å² buried · 43 hydrogen bonds · protein-protein
C–D · 648 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 372 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

1WBQ · ZnMg substituted aminopeptidase P from E. coli · the same entry in another collection · chain D against D, TM-score 1.00
P15034 · AlphaFold monomer V2.0 prediction for xaa-pro aminopeptidase (P15034) · a predicted model of the same protein · chain D 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 P15034
Elsewhere: RCSB PDB 1WBQ · PDBe 1WBQ · UniProt P15034

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