MolNFT v1 · #47425 · protein

Uninhibited human mmp-8

2OY4 · Neutrophil collagenase: “Uninhibited human mmp-8”. X-ray diffraction, 2 ligands (CA, ZN), 3 pockets (best druggability 0.59). MolNFT v1 #47425 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2OY4
Type: protein
Length: 314 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neutrophil collagenase
EC: 3.4.24.34
UniProt: P22894
Ligands: CA, ZN
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Neutrophil collagenase (EC 3.4.24.34)	protein	157	25% helix, 16% strand	P22894

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, F
ZN · Zinc ion · metal · 4 copies · chains A, F

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

Pockets

3 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	290	0.59	0.78	43	empty
2	107	0.56	0.85	22	ZN
3	92	0.53	0.84	20	empty

Interfaces

1 interface between chains.

A–F · 242 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2OY4 · Uninhibited human MMP-8 · the same entry in another collection · chain A against A, TM-score 1.00
P22894 · AlphaFold monomer V2.0 prediction for neutrophil collagenase (P22894) · 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 P22894
Elsewhere: RCSB PDB 2OY4 · PDBe 2OY4 · UniProt P22894

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