MolNFT v1 · #101655 · protein
Structure of vibrio cholerae chitin de-N-acetylase in complex with acetate ion (act) in P 21
4NY2 · Deacetylase DA1: “Structure of vibrio cholerae chitin de-N-acetylase in complex with acetate ion (act) in P 21”. X-ray diffraction, 2 ligands (ZN, CA), 9 pockets (best druggability 0.83). MolNFT v1 #101655 on GenesisL1: 3D…
- PDB
- 4NY2
- Type
- protein
- Length
- 807 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
- ZN, CA
- Pockets
- 9 · 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 | 404 | 30% helix, 21% strand | M7M1G8 |
| B | Deacetylase DA1 (EC 3.5.1.41) | protein | 403 | 31% helix, 21% strand | M7M1G8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.83 | 0.84 | 91 | GOL |
| 2 | 600 | 0.73 | 0.80 | 54 | ZN, ACT |
| 3 | 582 | 0.71 | 0.79 | 54 | ACT |
| 4 | 391 | 0.62 | 0.77 | 46 | empty |
| 5 | 154 | 0.56 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1651 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4NY2 · Structure of Vibrio cholerae chitin de-N-acetylase in complex with acetate ion (ACT) in P… · the same entry in another collection · chain B against B, 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 4NY2 · PDBe 4NY2 · UniProt M7M1G8
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