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 v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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.
| Volume (ų) | 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 Ų 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
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
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