Research workbench
Mouse kynurenine aminotransferase III, re-refinement of the pdb structure 3E2Z
Analyse Mouse kynurenine aminotransferase III, re-refinement of the pdb structure 3E2Z in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VER
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kynurenine--oxoglutarate transaminase 3
- EC
- 2.6.1.7, 4.4.1.13, 2.6.1.63
- UniProt
- Q71RI9
- Ligands
- PLP, PMP, CA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kynurenine--oxoglutarate transaminase 3 (EC 2.6.1.7, 4.4.1.13, 2.6.1.63) | protein | 410 | 44% helix, 16% strand | Q71RI9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A, B
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.73 | 0.83 | 51 | PLP, EPE |
| 2 | 401 | 0.70 | 0.81 | 42 | PMP, EPE |
| 3 | 82 | 0.58 | 0.87 | 21 | empty |
| 4 | 111 | 0.46 | 0.79 | 24 | empty |
| 5 | 123 | 0.43 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2912 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5VER · Mouse kynurenine aminotransferase III, re-refinement of the pdb structure 3E2Z · the same entry in another collection · chain A against A, TM-score 1.00
- Q71RI9 · AlphaFold monomer V2.0 prediction for kynurenine--oxoglutarate transaminase 3 (Q71RI9) · a predicted model of the same protein · 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 Q71RI9
- Elsewhere: RCSB PDB 5VER · PDBe 5VER · UniProt Q71RI9
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