Research workbench
Structure of vibrio cholerae chitin de-N-acetylase in complex with 2- (acetylamino)-2-deoxy-a-D-glucopyranose (ndg) and zinc ion
Analyse Structure of vibrio cholerae chitin de-N-acetylase in complex with 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NZ4
- Type
- protein
- Length
- 806 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deacetylase DA1
- EC
- 3.5.1.41
- UniProt
- M7M1G8
- Ligands
- NDG, ZN, CA
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deacetylase DA1 (EC 3.5.1.41) | protein | 403 | 31% helix, 21% strand | M7M1G8 |
| B | Deacetylase DA1 (EC 3.5.1.41) | protein | 403 | 31% helix, 21% strand | M7M1G8 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.83 | 0.84 | 77 | GOL |
| 2 | 549 | 0.72 | 0.80 | 55 | ACT, NDG |
| 3 | 538 | 0.71 | 0.79 | 52 | ACT, NDG |
| 4 | 415 | 0.62 | 0.77 | 51 | empty |
| 5 | 163 | 0.57 | 0.82 | 33 | GOL |
Interfaces
1 interface between chains.
- A–B · 1632 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4NZ4 · Structure of Vibrio cholerae chitin de-N-acetylase in complex with… · 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 M7M1G8
- Elsewhere: RCSB PDB 4NZ4 · PDBe 4NZ4 · UniProt M7M1G8
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