Research workbench
Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-1 (TIMP-1)
Analyse Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V96
- Type
- protein
- Length
- 323 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Homo sapiens
- Molecule
- Metalloproteinase inhibitor 1; Stromelysin-2
- EC
- 3.4.24.22
- UniProt
- P01033, P09238
- Ligands
- CA, ZN, PO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metalloproteinase inhibitor 1 | protein | 164 | 22% helix, 37% strand | P01033 |
| B | Stromelysin-2 (EC 3.4.24.22) | protein | 159 | 29% helix, 19% strand | P09238 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 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 | 344 | 0.72 | 0.84 | 30 | PO4 |
| 2 | 484 | 0.70 | 0.80 | 57 | empty |
| 3 | 51 | 0.32 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1249 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3V96 · Complex of matrix metalloproteinase-10 catalytic domain (mmp-10CD) with tissue inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P09238 · AlphaFold monomer V2.0 prediction for stromelysin-2 (P09238) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P01033 · AlphaFold monomer V2.0 prediction for metalloproteinase inhibitor 1 (P01033) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P01033
- Every structure of UniProt P09238
- Elsewhere: RCSB PDB 3V96 · PDBe 3V96 · UniProt P01033 · UniProt P09238
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