MolNFT v1 · #163995 · protein
Diaminobutyrate acetyltransferase ecta from paenibacillus lautus in complex with its product adaba
6SJY · L-2,4-diaminobutyric acid acetyltransferase: “Diaminobutyrate acetyltransferase ecta from paenibacillus lautus in complex with its product adaba”. X-ray diffraction, 1 ligand (9YT), 6 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6SJY
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- 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
- D3EKC1
- Ligands
- 9YT
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-2,4-diaminobutyric acid acetyltransferase (EC 2.3.1.178) | protein | 167 | 35% helix, 27% strand | D3EKC1 |
| C | L-2,4-diaminobutyric acid acetyltransferase (EC 2.3.1.178) | protein | 162 | 36% helix, 28% strand | D3EKC1 |
| B | L-2,4-diaminobutyric acid acetyltransferase (EC 2.3.1.178) | protein | 175 | 35% helix, 26% strand | D3EKC1 |
Ligands and binding sites
- 9YT · (2~{S})-4-acetamido-2-azanyl-butanoic acid · ligand · 3 copies · chains A, C, B
- GOL · Glycerol · additive · 3 copies · chains A, C, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.78 | 0.83 | 73 | 9YT |
| 2 | 304 | 0.62 | 0.79 | 43 | GOL, 9YT |
| 3 | 288 | 0.62 | 0.80 | 42 | 9YT, TRS |
| 4 | 344 | 0.57 | 0.76 | 54 | empty |
| 5 | 201 | 0.55 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–B · 655 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 526 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6SJY · Diaminobutyrate acetyltransferase EctA from Paenibacillus lautus in complex with its… · 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 D3EKC1
- Elsewhere: RCSB PDB 6SJY · PDBe 6SJY · UniProt D3EKC1
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