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Crystal structure of pyrococcus horikoshii kynurenine aminotransferase in complex with pmp, gla, 4AD, 2OG, glu and kya
Analyse Crystal structure of pyrococcus horikoshii kynurenine aminotransferase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WX9
- Type
- protein
- Length
- 808 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein PH0207
- UniProt
- O57946
- Ligands
- PMP, AKG, G9A, 3EE, GLU, KYA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative uncharacterized protein PH0207 | protein | 404 | 48% helix, 15% strand | O57946 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains A, C
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, C
- G9A · (2E)-pent-2-enedioic acid · ligand · 2 copies · chains A, C
- 3EE · 4-(2-aminophenyl)-2,4-dioxobutanoic acid · ligand · 2 copies · chains A, C
- GLU · Glutamic acid · ligand · chains A
- KYA · 4-hydroxyquinoline-2-carboxylic acid · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.81 | 0.83 | 82 | PMP, G9A, 3EE, KYA |
| 2 | 972 | 0.80 | 0.81 | 92 | PMP, G9A, 3EE, GLU |
| 3 | 92 | 0.48 | 0.81 | 22 | empty |
| 4 | 65 | 0.30 | 0.74 | 19 | empty |
| 5 | 61 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 3617 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3WX9 · Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with… · the same entry in another collection · chain C against C, 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 O57946
- Elsewhere: RCSB PDB 3WX9 · PDBe 3WX9 · UniProt O57946
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