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Structure of vibrio cholerae chitin de-N-acetylase in complex with acetate ion (act) in P 2 21 21
Analyse Structure of vibrio cholerae chitin de-N-acetylase in complex with acetate ion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NYY
- Type
- protein
- Length
- 1,617 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deacetylase DA1
- EC
- 3.5.1.41
- UniProt
- M7M1G8
- Ligands
- ZN, NA
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Deacetylase DA1 (EC 3.5.1.41) | protein | 405 | 30% helix, 21% strand | M7M1G8 |
| B | Deacetylase DA1 (EC 3.5.1.41) | protein | 403 | 31% helix, 21% strand | M7M1G8 |
| C | Deacetylase DA1 (EC 3.5.1.41) | protein | 404 | 30% helix, 21% strand | M7M1G8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.83 | 0.84 | 97 | EDO |
| 2 | 1193 | 0.83 | 0.84 | 98 | empty |
| 3 | 629 | 0.72 | 0.79 | 59 | ACT, EDO |
| 4 | 621 | 0.71 | 0.79 | 57 | ZN, ACT |
| 5 | 627 | 0.71 | 0.79 | 56 | ZN, ACT, EDO |
Interfaces
3 interfaces between chains.
- A–B · 1678 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1669 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 357 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4NYY · Structure of Vibrio cholerae chitin de-N-acetylase in complex with acetate ion (ACT) in P… · 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 4NYY · PDBe 4NYY · UniProt M7M1G8
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