Research workbench
Crystal structure of clostridium histolyticum colh collagenase collagen binding domain 3 at 2.2 ångström resolution in the presence of calcium and cadmium
Analyse Crystal structure of clostridium histolyticum colh collagenase collagen binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JQX
- 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
- CD, CA
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colh protein (EC 3.4.24.3) | protein | 117 | 0% helix, 55% strand | Q46085 |
| B | Colh protein (EC 3.4.24.3) | protein | 120 | 3% helix, 54% strand | Q46085 |
| C | Colh protein (EC 3.4.24.3) | protein | 121 | 2% helix, 53% strand | Q46085 |
Ligands and binding sites
- CD · Cadmium ion · metal · 9 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.66 | 0.76 | 87 | empty |
Interfaces
3 interfaces between chains.
- A–B · 484 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 406 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 240 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3JQX · Crystal structure of Clostridium histolyticum colH collagenase collagen binding domain 3… · the same entry in another collection · chain A against A, 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 3JQX · PDBe 3JQX · UniProt Q46085
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