Research workbench
Crystal structure of L-2,4-diaminobutyric acid acetyltransferase from bordetella parapertussis
Analyse Crystal structure of L-2,4-diaminobutyric acid acetyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D3S
- Type
- protein
- Length
- 606 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-2,4-diaminobutyric acid acetyltransferase
- EC
- 2.3.1.178
- UniProt
- Q7W980
- Ligands
- DAB, SO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-2,4-diaminobutyric acid acetyltransferase (EC 2.3.1.178) | protein | 159 | 36% helix, 29% strand | Q7W980 |
| B | L-2,4-diaminobutyric acid acetyltransferase (EC 2.3.1.178) | protein | 153 | 34% helix, 31% strand | Q7W980 |
| C | L-2,4-diaminobutyric acid acetyltransferase (EC 2.3.1.178) | protein | 149 | 37% helix, 30% strand | Q7W980 |
| D | L-2,4-diaminobutyric acid acetyltransferase (EC 2.3.1.178) | protein | 145 | 35% helix, 29% strand | Q7W980 |
Ligands and binding sites
- DAB · 2,4-diaminobutyric acid · ligand · 2 copies · chains C, D, A, B
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.80 | 0.81 | 118 | SO4, GOL |
| 2 | 54 | 0.71 | 0.98 | 12 | DAB |
| 3 | 56 | 0.71 | 0.97 | 12 | DAB |
| 4 | 315 | 0.59 | 0.77 | 34 | SO4 |
| 5 | 140 | 0.50 | 0.79 | 25 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1463 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1181 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 285 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 245 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 152 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3D3S · Crystal structure of L-2,4-diaminobutyric acid acetyltransferase from Bordetella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7W980 · AlphaFold monomer V2.0 prediction for L-2,4-diaminobutyric acid acetyltransferase (Q7W980) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q7W980
- Elsewhere: RCSB PDB 3D3S · PDBe 3D3S · UniProt Q7W980
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