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The first crystal structure of the daba aminotransferase ectb in the ectoine biosynthesis pathway of the model organism chromohalobacter salexigens dsm 3034
Analyse The first crystal structure of the daba aminotransferase ectb in the ectoine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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