Research workbench
Human stromelysin-1 (E202Q) catalytic domain complexed with ro-26-2812
Analyse Human stromelysin-1 (E202Q) catalytic domain complexed with ro-26-2812 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C8T
- Type
- protein
- Length
- 334 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
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Stromelysin-1 (EC 3.4.24.17) | protein | 167 | 26% helix, 16% 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 · 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.74 | 0.83 | 40 | empty |
| 2 | 179 | 0.65 | 0.85 | 28 | TR1 |
| 3 | 155 | 0.61 | 0.84 | 26 | TR1 |
| 4 | 74 | 0.40 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 916 Ų buried · 3 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 1C8T · PDBe 1C8T · UniProt P08254
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