Research workbench
Complex of matrix metalloproteinase-10 catalytic domain (mmp-10CD) with tissue inhibitor of metalloproteinases-2 (timp-2)
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
- 4ILW
- Type
- protein
- Length
- 682 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metalloproteinase inhibitor 2; Stromelysin-2
- EC
- 3.4.24.22
- UniProt
- P16035, P09238
- Ligands
- CA, ZN
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metalloproteinase inhibitor 2 | protein | 182 | 18% helix, 37% strand | P16035 |
| D, F | Stromelysin-2 (EC 3.4.24.22) | protein | 159 | 25% helix, 18% strand | P09238 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains D, F
- ZN · Zinc ion · metal · 4 copies · chains A, D, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.81 | 0.82 | 109 | empty |
| 2 | 335 | 0.62 | 0.78 | 45 | empty |
| 3 | 258 | 0.58 | 0.78 | 30 | empty |
| 4 | 249 | 0.57 | 0.78 | 34 | empty |
| 5 | 176 | 0.52 | 0.78 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1315 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1161 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 184 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 110 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4ILW · 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 D against A, TM-score 0.98
- P16035 · AlphaFold monomer V2.0 prediction for metalloproteinase inhibitor 2 (P16035) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P16035
- Every structure of UniProt P09238
- Elsewhere: RCSB PDB 4ILW · PDBe 4ILW · UniProt P16035 · UniProt P09238
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