Research workbench
(R)-selective amine transaminase from exophiala sideris
Analyse (R)-selective amine transaminase from exophiala sideris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SNL
- Type
- protein
- Length
- 1,911 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine transaminase
- UniProt
- A0A0D1XFW6
- Ligands
- PLP, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Amine transaminase | protein | 318 | 34% helix, 29% strand | A0A0D1XFW6 |
| C | Amine transaminase | protein | 318 | 33% helix, 28% strand | A0A0D1XFW6 |
| D | Amine transaminase | protein | 320 | 33% helix, 28% strand | A0A0D1XFW6 |
| E | Amine transaminase | protein | 319 | 34% helix, 27% strand | A0A0D1XFW6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains C, F
- GOL · Glycerol · additive · 2 copies · chains A, D, E, B
- P6G · Hexaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.81 | 0.82 | 118 | PLP |
| 2 | 1193 | 0.81 | 0.82 | 113 | GOL |
| 3 | 378 | 0.76 | 0.86 | 50 | PLP |
| 4 | 85 | 0.75 | 0.97 | 27 | PLP |
| 5 | 454 | 0.73 | 0.82 | 64 | empty |
Interfaces
10 interfaces between chains.
- A–D · 2244 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 2236 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 821 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 508 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 319 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6SNL · (R)-selective amine transaminase from Exophiala sideris · 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 A0A0D1XFW6
- Elsewhere: RCSB PDB 6SNL · PDBe 6SNL · UniProt A0A0D1XFW6
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