MolNFT v1 · #33986 · protein
Stromelysin-1 (mmp-3) complexed to a hydroxamic acid inhibitor
2D1O: “Stromelysin-1 (mmp-3) complexed to a hydroxamic acid inhibitor”. X-ray diffraction, 3 ligands (FA4, CA, ZN), 1 pocket (best druggability 0.76). MolNFT v1 #33986 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2D1O
- Type
- protein
- Length
- 339 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
- FA4, CA, ZN
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stromelysin-1 (EC 3.4.24.17) | protein | 171 | 25% helix, 18% strand | P08254 |
| B | Stromelysin-1 (EC 3.4.24.17) | protein | 168 | 26% helix, 18% strand | P08254 |
Ligands and binding sites
- FA4 · Sm-25453 · 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.76 | 0.83 | 69 | ZN, FA4 |
Interfaces
1 interface between chains.
- A–B · 723 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
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 2D1O · PDBe 2D1O · UniProt P08254
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