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Matrilysin complexed with carboxylate inhibitor

Analyse Matrilysin complexed with carboxylate inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MMP
Type: protein
Length: 332 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gelatinase a
EC: 3.4.24.23
UniProt: P09237
Ligands: RSS, ZN, CA
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Gelatinase a (EC 3.4.24.23)	protein	166	24% helix, 18% strand	P09237

Ligands and binding sites

RSS · 5-methyl-3-(9-oxo-1,8-diaza-tricyclo[10.6.1.013,18]nonadeca-12(19),13,15,17-tetraen-10-ylcarbamoyl)-hexanoic acid · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 4 copies · chains A, B
CA · Calcium ion · metal · 4 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	493	0.65	0.77	42	empty
2	89	0.43	0.79	20	ZN, RSS
3	64	0.39	0.80	17	ZN

Interfaces

1 interface between chains.

A–B · 215 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1MMP · Matrilysin complexed with carboxylate inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P09237 · AlphaFold monomer V2.0 prediction for matrilysin (P09237) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P09237
Elsewhere: RCSB PDB 1MMP · PDBe 1MMP · UniProt P09237

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