Research workbench
Crystal structure of the peptidase domain of collagenase H from clostridium histolyticum in complex with the peptidic inhibitor isoamylphosphonyl-gly-pro-ala at 1.77 ångström resolution.
Analyse Crystal structure of the peptidase domain of collagenase H from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ARF
- Type
- protein
- Length
- 383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colh protein; Isoamylphosphonyl-gly-pro-ala
- EC
- 3.4.24.3
- UniProt
- Q46085
- Ligands
- IP8, ZN, CA
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colh protein (EC 3.4.24.3) | protein | 380 | 48% helix, 19% strand | Q46085 |
| B | Isoamylphosphonyl-gly-pro-ala | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- IP8 · Isopentenyl phosphate · ligand · chains A, B
- ZN · Zinc ion · metal · chains A, B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.66 | 0.84 | 29 | empty |
| 2 | 214 | 0.59 | 0.80 | 28 | IP8 |
| 3 | 63 | 0.38 | 0.79 | 17 | empty |
| 4 | 77 | 0.34 | 0.75 | 17 | empty |
| 5 | 55 | 0.34 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 284 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4ARF · 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 0.98
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 4ARF · PDBe 4ARF · UniProt Q46085
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