Research workbench
Crystal structure of human MMP1 catalytic domain at 2.2 a resolution
Analyse Crystal structure of human MMP1 catalytic domain at 2.2 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SHI
- Type
- protein
- Length
- 468 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interstitial collagenase
- EC
- 3.4.24.7
- UniProt
- P03956
- Ligands
- CA, ZN
- Pockets
- 8 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, M | Interstitial collagenase (EC 3.4.24.7) | protein | 156 | 25% helix, 16% strand | P03956 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, G, M
- ZN · Zinc ion · metal · 6 copies · chains A, G, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.42 | 0.77 | 25 | empty |
| 2 | 69 | 0.41 | 0.81 | 18 | empty |
| 3 | 130 | 0.40 | 0.74 | 23 | empty |
| 4 | 66 | 0.38 | 0.79 | 17 | empty |
| 5 | 69 | 0.37 | 0.78 | 16 | ZN |
Interfaces
2 interfaces between chains.
- A–G · 378 Ų buried · 8 hydrogen bonds · protein-protein
- A–M · 317 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3SHI · Crystal structure of human MMP1 catalytic domain at 2.2 A resolution · the same entry in another collection · chain A against A, 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
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
- Elsewhere: RCSB PDB 3SHI · PDBe 3SHI · UniProt P03956
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