Research workbench
Crystal structure of the clostridium histolyticum colh collagenase polycystic kidney disease-like domain 2A at 1.76 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
- 4U6T
- Type
- protein
- Length
- 344 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colh protein
- UniProt
- Q46085
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Colh protein | protein | 86 | 0% helix, 48% strand | Q46085 |
Ligands and binding sites
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.53 | 0.76 | 47 | empty |
| 2 | 52 | 0.45 | 0.84 | 19 | empty |
| 3 | 50 | 0.44 | 0.84 | 19 | empty |
| 4 | 60 | 0.42 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 527 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 514 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 507 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4U6T · Crystal structure of the Clostridium histolyticum colH collagenase polycystic kidney… · the same entry in another collection · chain D against D, 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 0.98
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 4U6T · PDBe 4U6T · UniProt Q46085
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