MolNFT v1 · #129001 · protein
Crystal structure of the peptidase domain of collagenase H from clostridium histolyticum in complex with N-aryl mercaptoacetamide- based inhibitor
5O7E · Colh protein: “Crystal structure of the peptidase domain of collagenase H from clostridium histolyticum in complex with…”. X-ray diffraction, 3 ligands (9NB, ZN, CA), 5 pockets (best druggability 0.67). MolNFT v1 #129001 on…
- PDB
- 5O7E
- Type
- protein
- Length
- 380 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colh protein
- UniProt
- Q46085
- Ligands
- 9NB, ZN, CA
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colh protein | protein | 380 | 49% helix, 19% strand | Q46085 |
Ligands and binding sites
- 9NB · ~{N}-(4-ethanoylphenyl)-2-sulfanyl-ethanamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.67 | 0.85 | 30 | empty |
| 2 | 306 | 0.62 | 0.79 | 37 | 9NB |
| 3 | 90 | 0.43 | 0.79 | 19 | empty |
| 4 | 61 | 0.38 | 0.80 | 19 | empty |
| 5 | 60 | 0.28 | 0.74 | 17 | empty |
Compared structures
- 5O7E · Crystal structure of the peptidase domain of collagenase H from Clostridium histolyticum… · 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 5O7E · PDBe 5O7E · UniProt Q46085
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