MolNFT v1 · #153087 · protein
GABA aminotransferase from corynebacterium glutamicum
6J2V · Plp-dependent aminotransferases: “GABA aminotransferase from corynebacterium glutamicum”. X-ray diffraction, 1 ligand (PLZ), 15 pockets (best druggability 0.83). MolNFT v1 #153087 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6J2V
- Type
- protein
- Length
- 1,760 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plp-dependent aminotransferases
- EC
- 2.6.1.19
- UniProt
- Q8NT35
- Ligands
- PLZ
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Plp-dependent aminotransferases (EC 2.6.1.19) | protein | 440 | 40% helix, 18% strand | Q8NT35 |
Ligands and binding sites
- PLZ · 4-[({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methyl)amino]butanoic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.83 | 0.84 | 127 | PLZ |
| 2 | 1200 | 0.82 | 0.83 | 127 | PLZ |
| 3 | 525 | 0.74 | 0.82 | 61 | PLZ |
| 4 | 488 | 0.73 | 0.82 | 56 | PLZ |
| 5 | 330 | 0.69 | 0.83 | 47 | GOL |
Interfaces
6 interfaces between chains.
- C–D · 4487 Ų buried · 86 hydrogen bonds · protein-protein
- A–B · 4485 Ų buried · 84 hydrogen bonds · protein-protein
- A–C · 782 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 776 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6J2V · GABA aminotransferase from Corynebacterium glutamicum · the same entry in another collection · chain A 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 Q8NT35
- Elsewhere: RCSB PDB 6J2V · PDBe 6J2V · UniProt Q8NT35
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