Research workbench

Structure of MMP3 complexed with a platinum-based inhibitor.

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

PDB: 4DPE
Type: protein
Length: 335 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.96
Source: Homo sapiens
Molecule: Stromelysin-1
EC: 3.4.24.17
UniProt: P08254
Ligands: NGH, CA, PT, ZN, CL
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · resolution 1.96 · 2 distinct chains · 24% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Stromelysin-1 (EC 3.4.24.17)	protein	168	24% helix, 17% strand	P08254
B	Stromelysin-1 (EC 3.4.24.17)	protein	167	23% helix, 17% strand	P08254

Ligands and binding sites

NGH · N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid · ligand · chains B
CA · Calcium ion · metal · 6 copies · chains A, B
PT · Platinum (II) ion · metal · 6 copies · chains A, B
ZN · Zinc ion · metal · 4 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains 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	140	0.61	0.85	24	empty
2	217	0.57	0.79	34	NGH
3	195	0.45	0.74	30	empty

Interfaces

1 interface between chains.

A–B · 544 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4DPE · Structure of MMP3 complexed with a platinum-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 4DPE · PDBe 4DPE · UniProt P08254

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.