MolNFT v1 · #68269 · protein
Crystal structure of clostridium histolyticum colh collagenase collagen-binding domain 3 at 2 ångström resolution in presence of calcium
3JQW · Colh protein: “Crystal structure of clostridium histolyticum colh collagenase collagen-binding domain 3 at 2 ångström…”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.62). MolNFT v1 #68269 on GenesisL1: 3D…
- PDB
- 3JQW
- Type
- protein
- Length
- 358 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colh protein
- EC
- 3.4.24.3
- UniProt
- Q46085
- Ligands
- CA
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colh protein (EC 3.4.24.3) | protein | 117 | 3% helix, 55% strand | Q46085 |
| B | Colh protein (EC 3.4.24.3) | protein | 120 | 3% helix, 58% strand | Q46085 |
| C | Colh protein (EC 3.4.24.3) | protein | 121 | 2% helix, 57% strand | Q46085 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.62 | 0.76 | 66 | empty |
| 2 | 238 | 0.54 | 0.77 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 453 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 371 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 274 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3JQW · Crystal structure of Clostridium histolyticum colH collagenase collagen-binding domain 3… · the same entry in another collection · chain B against B, TM-score 1.00
- Q46085 · AlphaFold monomer V2.0 prediction for collagenase colh (Q46085) · 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 Q46085
- Elsewhere: RCSB PDB 3JQW · PDBe 3JQW · UniProt Q46085
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