MolNFT v1 · #94206 · protein
Crystal structure of clostridium histolyticum colg collagenase collagen-binding domain 3B at 1.35 ångström resolution in presence of calcium nitrate
4HPK: “Crystal structure of clostridium histolyticum colg collagenase collagen-binding domain 3B at 1.35 ångström…”. X-ray diffraction, 3 ligands (CA, CL, NO3), 1 pocket (best druggability 0.43). MolNFT v1 #94206 on GenesisL1: 3D…
- PDB
- 4HPK
- Type
- protein
- Length
- 223 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase
- UniProt
- Q9X721
- Ligands
- CA, CL, NO3
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase | protein | 110 | 3% helix, 60% strand | Q9X721 |
| B | Collagenase | protein | 113 | 3% helix, 62% strand | Q9X721 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
- NO3 · Nitrate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.43 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 717 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4HPK · Crystal structure of Clostridium histolyticum colg collagenase collagen-binding domain 3B… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X721 · AlphaFold monomer V2.0 prediction for collagenase colg (Q9X721) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9X721
- Elsewhere: RCSB PDB 4HPK · PDBe 4HPK · UniProt Q9X721
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