MolNFT v1 · #23901 · protein
Mmp-3/TIMP-1 complex
1UEA · Matrix metalloproteinase-3: “Mmp-3/TIMP-1 complex”. X-ray diffraction, 2 ligands (CA, ZN), 11 pockets (best druggability 0.71). MolNFT v1 #23901 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1UEA
- Type
- protein
- Length
- 698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metalloproteinase-3; Tissue inhibitor of metalloproteinase-1
- EC
- 3.4.24.17
- UniProt
- P08254, P01033
- Ligands
- CA, ZN
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Matrix metalloproteinase-3 (EC 3.4.24.17) | protein | 168 | 25% helix, 18% strand | P08254 |
| B, D | Tissue inhibitor of metalloproteinase-1 | protein | 181 | 18% helix, 35% strand | P01033 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.71 | 0.80 | 70 | empty |
| 2 | 533 | 0.71 | 0.80 | 58 | empty |
| 3 | 376 | 0.67 | 0.80 | 32 | empty |
| 4 | 355 | 0.65 | 0.79 | 31 | empty |
| 5 | 191 | 0.64 | 0.84 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1364 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1288 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 308 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 modified (disulfide, engineered).
Compared structures
- 1UEA · Mmp-3/TIMP-1 complex · 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 0.95
- P01033 · AlphaFold monomer V2.0 prediction for metalloproteinase inhibitor 1 (P01033) · a predicted model of the same protein · chain B against A, TM-score 0.93
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
- Every structure of UniProt P01033
- Elsewhere: RCSB PDB 1UEA · PDBe 1UEA · UniProt P08254 · UniProt P01033
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