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Crystal structure of MMP3 complexed with a thiazepine based inhibitor.

Analyse Crystal structure of MMP3 complexed with a thiazepine based inhibitor. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1D5J
Type: protein
Length: 342 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stromelysin-1
EC: 3.4.24.17
UniProt: P08254
Ligands: MM3, CA, ZN
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Stromelysin-1 (EC 3.4.24.17)	protein	169	24% helix, 18% strand	P08254
B	Stromelysin-1 (EC 3.4.24.17)	protein	173	22% helix, 16% strand	P08254

Ligands and binding sites

MM3 · N-hydroxy-4-[(4-methoxylphenyl)sulfonyl]-2,2-dimethyl-hexahydro-1,4-thiazepine-3(S)-carboxamide · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 6 copies · chains A, B
ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

4 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	395	0.71	0.82	45	empty
2	212	0.57	0.79	32	ZN, MM3
3	146	0.47	0.77	31	ZN, MM3
4	53	0.33	0.78	15	empty

Interfaces

1 interface between chains.

A–B · 593 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1D5J · Crystal structure of MMP3 complexed with a thiazepine based inhibitor. · the same entry in another collection · chain A against A, TM-score 1.00
P08254 · AlphaFold monomer V2.0 prediction for stromelysin-1 (P08254) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P08254
Elsewhere: RCSB PDB 1D5J · PDBe 1D5J · UniProt P08254

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