Research workbench
Hkatii in complex with ligand (2R)-N-benzyl-1-[6-methyl-5-(oxan-4-yl)- 7-oxo-6H,7H-[1,3]THIAZOLO[5,4-D]PYRIMIDIN-2-YL]PYRROLIDINE-2- carboxamide
Analyse Hkatii in complex with ligand (2R)-N-benzyl-1-[6-methyl-5-(oxan-4-yl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T8P
- Type
- protein
- Length
- 828 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KYNURENINE/ALPHA-aminoadipate aminotransferase, mitochondrial
- EC
- 2.6.1.39, 2.6.1.7
- UniProt
- Q8N5Z0
- Ligands
- MVT, IOD
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KYNURENINE/ALPHA-aminoadipate aminotransferase, mitochondrial (EC 2.6.1.39, 2.6.1.7) | protein | 409 | 42% helix, 18% strand | Q8N5Z0 |
| B | KYNURENINE/ALPHA-aminoadipate aminotransferase, mitochondrial (EC 2.6.1.39, 2.6.1.7) | protein | 419 | 44% helix, 17% strand | Q8N5Z0 |
Ligands and binding sites
- MVT · 3,5-bis(fluoranyl)-~{N}-[5-[(2~{R})-2-(3-fluorophenyl)-3-methyl-butyl]-1,3,4-thiadiazol-2-yl]benzenesulfonamide · ligand · 4 copies · chains A, B
- IOD · Iodide ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.72 | 0.80 | 47 | MVT, IOD |
| 2 | 449 | 0.68 | 0.79 | 37 | MVT, IOD |
| 3 | 296 | 0.67 | 0.82 | 33 | empty |
| 4 | 70 | 0.42 | 0.80 | 16 | empty |
| 5 | 55 | 0.41 | 0.82 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3746 Ų buried · 69 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 6T8P · HKATII IN COMPLEX WITH LIGAND (2R)-N-benzyl-1-[6-methyl-5-(oxan-4-yl)-7-oxo-6H,7H-[1,3]thi… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N5Z0 · AlphaFold monomer V2.0 prediction for KYNURENINE/ALPHA-aminoadipate aminotransferase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8N5Z0
- Elsewhere: RCSB PDB 6T8P · PDBe 6T8P · UniProt Q8N5Z0
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