Research workbench
Structure of vibrio cholerae chitin de-N-acetylase in complex with DI(N-acetyl-D-glucosamine) (cbs) in P 21
Analyse Structure of vibrio cholerae chitin de-N-acetylase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NZ1
- 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
- NAG, CA, ZN, CL
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deacetylase DA1 (EC 3.5.1.41) | protein | 403 | 32% helix, 19% strand | M7M1G8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · 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 | 1096 | 0.84 | 0.85 | 80 | CA, EDO |
| 2 | 430 | 0.74 | 0.84 | 56 | NAG, ZN |
| 3 | 600 | 0.72 | 0.79 | 53 | ZN |
| 4 | 293 | 0.60 | 0.79 | 50 | empty |
| 5 | 127 | 0.59 | 0.85 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1607 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4NZ1 · 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 4NZ1 · PDBe 4NZ1 · UniProt M7M1G8
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