Research workbench
Crystal structure of the clostridium histolyticum colh collagenase polycystic kidney disease-like domain 2A in the presence of calcium at 1.9 ångström resolution
Analyse Crystal structure of the clostridium histolyticum colh collagenase polycystic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U7K
- Type
- protein
- Length
- 688 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colh protein
- UniProt
- Q46085
- Ligands
- CA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Colh protein | protein | 86 | 0% helix, 50% strand | Q46085 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.80 | 0.82 | 125 | empty |
| 2 | 174 | 0.59 | 0.82 | 50 | empty |
| 3 | 189 | 0.57 | 0.81 | 46 | empty |
| 4 | 171 | 0.48 | 0.76 | 25 | empty |
| 5 | 162 | 0.43 | 0.75 | 24 | empty |
Interfaces
13 interfaces between chains.
- A–D · 508 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 503 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 495 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 493 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 314 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4U7K · Crystal structure of the Clostridium histolyticum colH collagenase polycystic kidney… · the same entry in another collection · chain H against H, TM-score 1.00
- Q46085 · AlphaFold monomer V2.0 prediction for collagenase colh (Q46085) · a predicted model of the same protein · chain D 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 4U7K · PDBe 4U7K · UniProt Q46085
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.