MolNFT v1 · #61116 · protein
Crystal structure of kynurenine aminotransferase II complex with alpha-ketoglutarate
3DC1 · KYNURENINE/ALPHA-aminoadipate aminotransferase mitochondrial: “Crystal structure of kynurenine aminotransferase II complex with alpha-ketoglutarate”. X-ray diffraction, 1 ligand (AKG), 14 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 3DC1
- Type
- protein
- Length
- 1,675 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KYNURENINE/ALPHA-aminoadipate aminotransferase mitochondrial
- EC
- 2.6.1.7, 2.6.1.39
- UniProt
- Q8N5Z0
- Ligands
- AKG
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KYNURENINE/ALPHA-aminoadipate aminotransferase mitochondrial (EC 2.6.1.7, 2.6.1.39) | protein | 415 | 42% helix, 18% strand | Q8N5Z0 |
| B | KYNURENINE/ALPHA-aminoadipate aminotransferase mitochondrial (EC 2.6.1.7, 2.6.1.39) | protein | 417 | 42% helix, 18% strand | Q8N5Z0 |
| C | KYNURENINE/ALPHA-aminoadipate aminotransferase mitochondrial (EC 2.6.1.7, 2.6.1.39) | protein | 425 | 41% helix, 17% strand | Q8N5Z0 |
| D | KYNURENINE/ALPHA-aminoadipate aminotransferase mitochondrial (EC 2.6.1.7, 2.6.1.39) | protein | 418 | 41% helix, 17% strand | Q8N5Z0 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.70 | 0.78 | 65 | empty |
| 2 | 284 | 0.67 | 0.83 | 33 | empty |
| 3 | 288 | 0.67 | 0.83 | 29 | empty |
| 4 | 216 | 0.64 | 0.83 | 36 | GOL |
| 5 | 205 | 0.62 | 0.83 | 32 | GOL |
Interfaces
4 interfaces between chains.
- C–D · 4145 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 3934 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 679 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 91 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 3DC1 · Crystal structure of kynurenine aminotransferase II complex with alpha-ketoglutarate · 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 0.99
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 Q8N5Z0
- Elsewhere: RCSB PDB 3DC1 · PDBe 3DC1 · UniProt Q8N5Z0
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