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
- 4JA1
- Type
- protein
- Length
- 335 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
- NGH, CA, ZN, PT, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 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 | 25% helix, 18% 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
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PT · Platinum (II) ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.69 | 0.82 | 44 | empty |
| 2 | 231 | 0.59 | 0.80 | 36 | NGH |
| 3 | 230 | 0.55 | 0.78 | 32 | empty |
| 4 | 60 | 0.33 | 0.76 | 13 | empty |
| 5 | 50 | 0.29 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 615 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4JA1 · Structure of MMP3 complexed with a platinum-based inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 4JA1 · PDBe 4JA1 · UniProt P08254
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