MolNFT v1 · #84861 · protein

Mmp-13 complexed with 2-napthylsulfonamide hydroxamic acid inhibitor

3ZXH · Collagenase 3: “Mmp-13 complexed with 2-napthylsulfonamide hydroxamic acid inhibitor”. X-ray diffraction, 3 ligands (E41, CA, ZN), 3 pockets (best druggability 0.71). MolNFT v1 #84861 on GenesisL1: 3D structure, binding sites and…

PDB: 3ZXH
Type: protein
Length: 332 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Collagenase 3
EC: 3.4.24.-
UniProt: P45452
Ligands: E41, CA, ZN
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Collagenase 3 (EC 3.4.24.-)	protein	166	24% helix, 18% strand	P45452
B	Collagenase 3 (EC 3.4.24.-)	protein	166	24% helix, 18% strand	P45452

Ligands and binding sites

E41 · N-hydroxy-N^2^-(3-methylbutyl)-N^2^-(naphthalen-2-ylsulfonyl)-D-valinamide · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 7 copies · chains A, B
ZN · Zinc ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · 5 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	868	0.71	0.76	88	ZN, E41, GOL
2	177	0.55	0.79	30	ZN, E41, GOL
3	53	0.27	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 1247 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3ZXH · MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P45452 · AlphaFold monomer V2.0 prediction for collagenase 3 (P45452) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P45452
Elsewhere: RCSB PDB 3ZXH · PDBe 3ZXH · UniProt P45452

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