Research workbench
The cyrstal structure of TAURINE:2-oxoglutarate aminotransferase from bifidobacterium kashiwanohense, in complex with plp and glutamate
Analyse The cyrstal structure of TAURINE:2-oxoglutarate aminotransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JIX
- Type
- protein
- Length
- 1,785 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TAURINE:2-oxoglutarate aminotransferase
- UniProt
- A0A0A7I435
- Ligands
- GGL, PLP
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D | TAURINE:2-oxoglutarate aminotransferase | protein | 446 | 43% helix, 19% strand | A0A0A7I435 |
| A | TAURINE:2-oxoglutarate aminotransferase | protein | 447 | 42% helix, 19% strand | A0A0A7I435 |
Ligands and binding sites
- GGL · Gamma-L-glutamic acid · ligand · 8 copies · chains B, D, A, C
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.86 | 0.87 | 129 | GGL, PLP |
| 2 | 1163 | 0.85 | 0.85 | 130 | GGL, PLP |
| 3 | 115 | 0.78 | 0.97 | 28 | empty |
| 4 | 114 | 0.77 | 0.96 | 19 | empty |
| 5 | 137 | 0.73 | 0.92 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–D · 4974 Ų buried · 77 hydrogen bonds · protein-protein
- A–C · 4924 Ų buried · 80 hydrogen bonds · protein-protein
- C–D · 1106 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 1095 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 74 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6JIX · The cyrstal structure of taurine:2-oxoglutarate aminotransferase from Bifidobacterium… · 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 A0A0A7I435
- Elsewhere: RCSB PDB 6JIX · PDBe 6JIX · UniProt A0A0A7I435
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