MolNFT v1 · #83918 · protein
Crystal structure of cod
3WX7 · Chitin oligosaccharide deacetylase: “Crystal structure of cod”. X-ray diffraction, 2 ligands (CA, ZN), 5 pockets (best druggability 0.83). MolNFT v1 #83918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WX7
- Type
- protein
- Length
- 804 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitin oligosaccharide deacetylase
- UniProt
- A6P4T5
- Ligands
- CA, ZN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chitin oligosaccharide deacetylase | protein | 402 | 31% helix, 20% strand | A6P4T5 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.83 | 0.86 | 90 | GOL |
| 2 | 532 | 0.71 | 0.80 | 55 | ACT |
| 3 | 572 | 0.71 | 0.79 | 53 | ZN, ACT |
| 4 | 170 | 0.45 | 0.75 | 28 | empty |
| 5 | 80 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1454 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3WX7 · Crystal structure of COD · 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 A6P4T5
- Elsewhere: RCSB PDB 3WX7 · PDBe 3WX7 · UniProt A6P4T5
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