MolNFT v1 · #104987 · protein

Crystal structure of E COLI pepq

4QR8 · Xaa-pro dipeptidase: “Crystal structure of E COLI pepq”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.80). MolNFT v1 #104987 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QR8
Type: protein
Length: 882 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xaa-pro dipeptidase
EC: 3.4.13.9
UniProt: P21165
Ligands: MG
Pockets: 12 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Xaa-pro dipeptidase (EC 3.4.13.9)	protein	441	38% helix, 17% strand	P21165

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	472	0.80	0.88	61	empty
2	301	0.79	0.90	44	empty
3	235	0.73	0.88	31	empty
4	153	0.43	0.75	21	empty
5	118	0.39	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 2444 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

4QR8 · Crystal Structure of E coli pepQ · the same entry in another collection · chain A against A, TM-score 1.00
P21165 · AlphaFold monomer V2.0 prediction for xaa-pro dipeptidase (P21165) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P21165
Elsewhere: RCSB PDB 4QR8 · PDBe 4QR8 · UniProt P21165

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