MolNFT v1 · #2662 · protein
Human stromelysin-1 catalytic domain complexed with ro-26-2812
1C3I: “Human stromelysin-1 catalytic domain complexed with ro-26-2812”. X-ray diffraction, 3 ligands (TR1, CA, ZN), 3 pockets (best druggability 0.71). MolNFT v1 #2662 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1C3I
- Type
- protein
- Length
- 343 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
- TR1, CA, ZN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stromelysin-1 (EC 3.4.24.17) | protein | 170 | 25% helix, 19% strand | P08254 |
| B | Stromelysin-1 (EC 3.4.24.17) | protein | 173 | 23% helix, 17% strand | P08254 |
Ligands and binding sites
- TR1 · 2-(2-{2-[(biphenyl-4-ylmethyl)-amino]-3-mercapto-pentanoylamino}-acetylamino)-3-methyl-butyric acid methyl ester · ligand · chains 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
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 | 351 | 0.71 | 0.84 | 45 | empty |
| 2 | 231 | 0.61 | 0.81 | 33 | ZN, TR1 |
| 3 | 51 | 0.25 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 591 Ų buried · 8 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 1C3I · PDBe 1C3I · UniProt P08254
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