MolNFT v1 · #156784 · protein
Crystal structure of 3-hydroxykynurenine transaminase from aedes aegypti
6MFB · Serine--pyruvate aminotransferase: “Crystal structure of 3-hydroxykynurenine transaminase from aedes aegypti”. X-ray diffraction, 1 ligand (PLP), 15 pockets (best druggability 0.78). MolNFT v1 #156784 on GenesisL1: 3D structure…
- PDB
- 6MFB
- Type
- protein
- Length
- 1,540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--pyruvate aminotransferase
- EC
- 2.6.1.44, 2.6.1.51
- UniProt
- Q0IG34
- Ligands
- PLP
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--pyruvate aminotransferase (EC 2.6.1.44, 2.6.1.51) | protein | 384 | 42% helix, 15% strand | Q0IG34 |
| C, B | Serine--pyruvate aminotransferase (EC 2.6.1.44, 2.6.1.51) | protein | 385 | 41% helix, 16% strand | Q0IG34 |
| D | Serine--pyruvate aminotransferase (EC 2.6.1.44, 2.6.1.51) | protein | 386 | 41% helix, 15% strand | Q0IG34 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.78 | 0.89 | 51 | empty |
| 2 | 275 | 0.78 | 0.90 | 50 | empty |
| 3 | 282 | 0.77 | 0.89 | 35 | empty |
| 4 | 55 | 0.72 | 0.99 | 17 | PLP |
| 5 | 50 | 0.68 | 0.97 | 20 | PLP |
Interfaces
6 interfaces between chains.
- C–D · 4005 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3945 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 607 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 587 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 172 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6MFB · Crystal structure of 3-hydroxykynurenine transaminase from Aedes aegypti · the same entry in another collection · chain A against A, TM-score 1.00
- Q0IG34 · AlphaFold monomer V2.0 prediction for 3-hydroxykynurenine transaminase (Q0IG34) · a predicted model of the same protein · chain D 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 Q0IG34
- Elsewhere: RCSB PDB 6MFB · PDBe 6MFB · UniProt Q0IG34
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