Research workbench
Collagenase from grimontia (vibrio) hollisae 1706B
Analyse Collagenase from grimontia (vibrio) hollisae 1706B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WSS
- Type
- protein
- Length
- 1,066 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microbial collagenase
- EC
- 3.4.24.3
- UniProt
- F7IZI6
- Ligands
- CA, ZN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Microbial collagenase (EC 3.4.24.3) | protein | 533 | 64% helix, 5% strand | F7IZI6 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains B
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 | 330 | 0.66 | 0.81 | 45 | ZN, PGE, PEG |
| 2 | 350 | 0.65 | 0.80 | 45 | ZN, EDO |
| 3 | 223 | 0.49 | 0.75 | 23 | empty |
| 4 | 81 | 0.33 | 0.74 | 22 | empty |
| 5 | 93 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 170 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7WSS · Collagenase from Grimontia (Vibrio) hollisae 1706B · the same entry in another collection · chain A against A, TM-score 1.00
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 F7IZI6
- Elsewhere: RCSB PDB 7WSS · PDBe 7WSS · UniProt F7IZI6
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