Research workbench
Crystal structure of the S84A mutant of antd, an N-acyltransferase from bacillus cereus in complex with dtdp-4-amino-4,6-dideoxyglucose and coenzyme a
Analyse Crystal structure of the S84A mutant of antd, an N-acyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VBK
- Type
- protein
- Length
- 558 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactoside O-acetyltransferase
- EC
- 2.3.1.18
- UniProt
- D7WGJ0
- Ligands
- COA, 0FX, BCT, CL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Galactoside O-acetyltransferase (EC 2.3.1.18) | protein | 186 | 13% helix, 39% strand | D7WGJ0 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 3 copies · chains A, E, C
- 0FX · dTDP-4-amino-4,6-dideoxyglucose · ligand · 3 copies · chains A, C, E
- BCT · Bicarbonate ion · ligand · 3 copies · chains A, C, E
- CL · Chloride ion · ion · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.75 | 0.84 | 55 | COA, 0FX, BCT |
| 2 | 418 | 0.74 | 0.83 | 64 | 0FX, BCT, COA |
| 3 | 403 | 0.72 | 0.83 | 53 | 0FX, BCT, COA |
Interfaces
3 interfaces between chains.
- A–E · 1458 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 1438 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1422 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3VBK · Crystal Structure of the S84A mutant of AntD, an N-acyltransferase from Bacillus cereus… · 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 D7WGJ0
- Elsewhere: RCSB PDB 3VBK · PDBe 3VBK · UniProt D7WGJ0
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