MolNFT v1 · #162855 · protein
The first crystal structure of the daba aminotransferase ectb in the ectoine biosynthesis pathway of the model organism chromohalobacter salexigens dsm 3034
6RL5 · Diaminobutyrate--2-oxoglutarate transaminase: “The first crystal structure of the daba aminotransferase ectb in the ectoine biosynthesis pathway of the…”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.83).…
- PDB
- 6RL5
- Type
- protein
- Length
- 3,346 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminobutyrate--2-oxoglutarate transaminase
- EC
- 2.6.1.76
- UniProt
- Q9ZEU7
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Diaminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.76) | protein | 417 | 40% helix, 18% strand | Q9ZEU7 |
| B, C | Diaminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.76) | protein | 419 | 41% helix, 18% strand | Q9ZEU7 |
| D, H | Diaminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.76) | protein | 417 | 39% helix, 17% strand | Q9ZEU7 |
| E | Diaminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.76) | protein | 418 | 42% helix, 17% strand | Q9ZEU7 |
| G | Diaminobutyrate--2-oxoglutarate transaminase (EC 2.6.1.76) | protein | 422 | 40% helix, 17% strand | Q9ZEU7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.83 | 0.96 | 36 | empty |
| 2 | 218 | 0.83 | 0.96 | 37 | empty |
| 3 | 210 | 0.83 | 0.96 | 38 | empty |
| 4 | 214 | 0.81 | 0.95 | 38 | empty |
| 5 | 1063 | 0.78 | 0.80 | 125 | PLP |
Interfaces
16 interfaces between chains.
- C–D · 4960 Ų buried · 68 hydrogen bonds · protein-protein
- G–H · 4936 Ų buried · 63 hydrogen bonds · protein-protein
- E–F · 4900 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 4850 Ų buried · 66 hydrogen bonds · protein-protein
- F–G · 1593 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6RL5 · The first crystal structure of the DABA aminotransferase EctB in the ectoine biosynthesis… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9ZEU7 · AlphaFold monomer V2.0 prediction for diaminobutyrate--2-oxoglutarate transaminase… · a predicted model of the same protein · chain G 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 Q9ZEU7
- Elsewhere: RCSB PDB 6RL5 · PDBe 6RL5 · UniProt Q9ZEU7
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