Research workbench
(R)-selective amine transaminase from shinella sp.
Analyse (R)-selective amine transaminase from shinella sp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XU3
- Type
- protein
- Length
- 1,285 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class IV aminotransferase
- UniProt
- A0A4Q8MG35
- Ligands
- PLP, PLG, GAB, NO3, CL
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class IV aminotransferase | protein | 320 | 33% helix, 27% strand | A0A4Q8MG35 |
| B | Class IV aminotransferase | protein | 321 | 33% helix, 25% strand | A0A4Q8MG35 |
| C, D | Class IV aminotransferase | protein | 322 | 34% helix, 27% strand | A0A4Q8MG35 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, D
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 2 copies · chains B, C
- GAB · 3-aminobenzoic acid · ligand · chains A, B, C
- NO3 · Nitrate ion · ion · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, D, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.85 | 0.89 | 100 | GOL, GAB |
| 2 | 477 | 0.78 | 0.85 | 62 | PLP |
| 3 | 518 | 0.78 | 0.85 | 64 | PLP |
| 4 | 531 | 0.77 | 0.84 | 62 | PLG, CL |
| 5 | 468 | 0.75 | 0.84 | 67 | PLG |
Interfaces
6 interfaces between chains.
- B–C · 2469 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2447 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 506 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 372 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6XU3 · (R)-selective amine transaminase from Shinella sp. · 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 A0A4Q8MG35
- Elsewhere: RCSB PDB 6XU3 · PDBe 6XU3 · UniProt A0A4Q8MG35
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