Research workbench
Crystal structure of antd, an N-acyltransferase from bacillus cereus in complex with dtdp-4-amino-4,6-dideoxyglucose and coenzyme a
Analyse Crystal structure of antd, an N-acyltransferase from bacillus cereus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VBI
- 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
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Galactoside O-acetyltransferase (EC 2.3.1.18) | protein | 186 | 12% helix, 38% 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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.80 | 0.81 | 122 | 0FX, BCT, COA |
| 2 | 480 | 0.73 | 0.82 | 56 | COA, 0FX, BCT |
Interfaces
3 interfaces between chains.
- C–E · 1465 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1428 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1411 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3VBI · Crystal Structure of AntD, an N-acyltransferase from Bacillus cereus 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 D7WGJ0
- Elsewhere: RCSB PDB 3VBI · PDBe 3VBI · UniProt D7WGJ0
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