Research workbench
X-ray structure of a novel matrix metalloproteinase inhibitor complexed to stromelysin
Analyse X-ray structure of a novel matrix metalloproteinase inhibitor complexed to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G4K
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stromelysin-1
- EC
- 3.4.24.17
- UniProt
- P08254
- Ligands
- HQQ, CA, ZN
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Stromelysin-1 (EC 3.4.24.17) | protein | 168 | 26% helix, 17% strand | P08254 |
Ligands and binding sites
- HQQ · 5-methyl-5-(4-phenoxy-phenyl)-pyrimidine-2,4,6-trione · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 9 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- GOL · Glycerol · additive · chains 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 | 538 | 0.70 | 0.79 | 48 | HQQ, GOL |
| 2 | 403 | 0.66 | 0.79 | 46 | HQQ |
| 3 | 187 | 0.54 | 0.79 | 33 | HQQ |
| 4 | 118 | 0.41 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 520 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 363 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1G4K · X-ray Structure of a Novel Matrix Metalloproteinase Inhibitor Complexed to Stromelysin · the same entry in another collection · chain A against A, TM-score 1.00
- P08254 · AlphaFold monomer V2.0 prediction for stromelysin-1 (P08254) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 1G4K · PDBe 1G4K · UniProt P08254
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