MolNFT v1 · #165811 · protein
RV3722C in complex with kynurenine
6U7A · Aminotransferase: “RV3722C in complex with kynurenine”. X-ray diffraction, 5 ligands (KYA, PMP, PLP), 20 pockets (best druggability 0.79). MolNFT v1 #165811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6U7A
- Type
- protein
- Length
- 3,382 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- UniProt
- A0A0E8TWE4
- Ligands
- KYA, PMP, PLP, Q0P, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, G | Aminotransferase | protein | 423 | 44% helix, 14% strand | A0A0E8TWE4 |
| D | Aminotransferase | protein | 429 | 45% helix, 14% strand | A0A0E8TWE4 |
| F | Aminotransferase | protein | 422 | 45% helix, 14% strand | A0A0E8TWE4 |
| H | Aminotransferase | protein | 416 | 44% helix, 14% strand | A0A0E8TWE4 |
Ligands and binding sites
- KYA · 4-hydroxyquinoline-2-carboxylic acid · ligand · 4 copies · chains A, B, C, H, D, E, F, G
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, H, D, E, F, G
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains D, E, F, G, C, H
- Q0P · (2S)-4-(2-aminophenyl)-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxobutanoic acid · ligand · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, H, C, D, F, G, E
- GOL · Glycerol · additive · 10 copies · chains A, D, F, B, C, G, H
- 1PE · Pentaethylene glycol · additive · 6 copies · chains A, D, B, C, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.79 | 0.85 | 101 | KYA, PMP |
| 2 | 374 | 0.76 | 0.86 | 64 | PLP |
| 3 | 82 | 0.75 | 0.98 | 20 | empty |
| 4 | 880 | 0.75 | 0.79 | 98 | GOL, 1PE |
| 5 | 79 | 0.74 | 0.97 | 19 | empty |
Interfaces
19 interfaces between chains.
- A–B · 2365 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2363 Ų buried · 44 hydrogen bonds · protein-protein
- C–H · 2359 Ų buried · 38 hydrogen bonds · protein-protein
- F–G · 2350 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 537 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6U7A · Rv3722c in complex with kynurenine · the same entry in another collection · chain E against E, 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 A0A0E8TWE4
- Elsewhere: RCSB PDB 6U7A · PDBe 6U7A · UniProt A0A0E8TWE4
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