MolNFT v1 · #101691 · protein
Structure of vibrio cholerae chitin de-N-acetylase in complex with DI(N-acetyl-D-glucosamine) (cbs) in P 21 21 21
4NZ3 · Deacetylase DA1: “Structure of vibrio cholerae chitin de-N-acetylase in complex with DI(N-acetyl-D-glucosamine) (cbs) in P 21…”. X-ray diffraction, 3 ligands (NAG, ZN, MG), 7 pockets (best druggability 0.85). MolNFT v1 #101691 on…
- PDB
- 4NZ3
- 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, ZN, MG
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deacetylase DA1 (EC 3.5.1.41) | protein | 403 | 30% helix, 20% strand | M7M1G8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.85 | 0.87 | 98 | EDO |
| 2 | 357 | 0.74 | 0.85 | 49 | NAG |
| 3 | 431 | 0.74 | 0.84 | 60 | NAG |
| 4 | 153 | 0.55 | 0.81 | 27 | EDO |
| 5 | 250 | 0.49 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1548 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4NZ3 · 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 4NZ3 · PDBe 4NZ3 · UniProt M7M1G8
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