Research workbench
Crystal structure of the catalytic domain of mmp-1 in complex with the inhibitory domain of timp-1
Analyse Crystal structure of the catalytic domain of mmp-1 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J0T
- Type
- protein
- Length
- 854 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interstitial collagenase; Metalloproteinase inhibitor 1
- EC
- 3.4.24.7
- UniProt
- P03956, P01033
- Ligands
- CA, ZN
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interstitial collagenase (EC 3.4.24.7) | protein | 161 | 25% helix, 17% strand | P03956 |
| B | Interstitial collagenase (EC 3.4.24.7) | protein | 162 | 24% helix, 17% strand | P03956 |
| C | Interstitial collagenase (EC 3.4.24.7) | protein | 159 | 25% helix, 18% strand | P03956 |
| D, E, F | Metalloproteinase inhibitor 1 | protein | 124 | 18% helix, 35% strand | P01033 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.63 | 0.82 | 33 | empty |
| 2 | 267 | 0.62 | 0.80 | 34 | empty |
| 3 | 189 | 0.61 | 0.83 | 31 | empty |
| 4 | 280 | 0.57 | 0.77 | 27 | empty |
| 5 | 227 | 0.51 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–E · 816 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 790 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 779 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 2J0T · Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain… · the same entry in another collection · chain F against F, TM-score 1.00
- P03956 · AlphaFold monomer V2.0 prediction for interstitial collagenase (P03956) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P01033 · AlphaFold monomer V2.0 prediction for metalloproteinase inhibitor 1 (P01033) · a predicted model of the same protein · chain D 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 P03956
- Every structure of UniProt P01033
- Elsewhere: RCSB PDB 2J0T · PDBe 2J0T · UniProt P03956 · UniProt P01033
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