MolNFT v1 · #179382 · protein

X-ray crystallographic structure model of lactococcus lactis prolidase mutant R293S

7K3U · Aminopeptidase P family protein: “X-ray crystallographic structure model of lactococcus lactis prolidase mutant R293S”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.74). MolNFT v1 #179382 on GenesisL1: 3D…

PDB: 7K3U
Type: protein
Length: 3,620 residues
Chains: 10
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: 20 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Aminopeptidase P family protein (EC 3.4.13.9)	protein	362	38% helix, 23% strand	A8WBX8

Ligands and binding sites

MN · Manganese (II) ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J
GOL · Glycerol · additive · 5 copies · chains A, B, C, D, G

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	798	0.74	0.79	83	empty
2	771	0.73	0.79	74	empty
3	1017	0.71	0.75	90	empty
4	408	0.64	0.78	51	empty
5	324	0.61	0.78	31	MN

Interfaces

14 interfaces between chains.

C–D · 850 Å² buried · 12 hydrogen bonds · protein-protein
H–I · 823 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 523 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 403 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 364 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7K3U · X-ray crystallographic structure model of Lactococcus lactis prolidase mutant R293S · 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 7K3U · PDBe 7K3U · UniProt A8WBX8

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