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Crystal structure of the S84T mutant of antd, an N-acyltransferase from bacillus cereus in complex with dtdp and coenzyme a
Analyse Crystal structure of the S84T 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
- 3VBM
- Type
- protein
- Length
- 568 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, TYD, BCT, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactoside O-acetyltransferase (EC 2.3.1.18) | protein | 187 | 12% helix, 37% strand | D7WGJ0 |
| C | Galactoside O-acetyltransferase (EC 2.3.1.18) | protein | 188 | 13% helix, 38% strand | D7WGJ0 |
| E | Galactoside O-acetyltransferase (EC 2.3.1.18) | protein | 193 | 14% helix, 36% strand | D7WGJ0 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 3 copies · chains A, C, E
- TYD · Thymidine-5'-diphosphate · 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 | 592 | 0.76 | 0.82 | 70 | COA, TYD, BCT |
| 2 | 468 | 0.73 | 0.82 | 53 | COA, TYD, BCT |
| 3 | 568 | 0.72 | 0.80 | 58 | COA, TYD, BCT |
Interfaces
3 interfaces between chains.
- A–E · 1562 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1499 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1419 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3VBM · Crystal Structure of the S84T 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 3VBM · PDBe 3VBM · UniProt D7WGJ0
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