MolNFT v1 · #169777 · protein

X-ray crystallographic structure model of lactococcus lactis prolidase mutant H38S

6XMR · Aminopeptidase P family protein: “X-ray crystallographic structure model of lactococcus lactis prolidase mutant H38S”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.59). MolNFT v1 #169777 on GenesisL1: 3D…

PDB: 6XMR
Type: protein
Length: 724 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminopeptidase P family protein
EC: 3.4.13.9
UniProt: A8WBX8
Ligands: MN
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aminopeptidase P family protein (EC 3.4.13.9)	protein	362	38% helix, 24% strand	A8WBX8

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B

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

Pockets

5 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	262	0.59	0.79	37	empty
2	359	0.55	0.74	53	empty
3	290	0.53	0.75	27	MN
4	223	0.49	0.75	26	empty
5	59	0.35	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 888 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6XMR · X-ray crystallographic structure model of Lactococcus lactis prolidase mutant H38S · 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 A8WBX8
Elsewhere: RCSB PDB 6XMR · PDBe 6XMR · UniProt A8WBX8

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