Research workbench
Crystal structure of an R-selective transaminase from thermomyces stellatus.
Analyse Crystal structure of an R-selective transaminase from thermomyces stellatus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XWB
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R-selective transaminase
- Ligands
- PLP, NA
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | R-selective transaminase | protein | 319 | 33% helix, 26% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.69 | 0.87 | 33 | empty |
| 2 | 71 | 0.67 | 0.94 | 25 | PLP |
| 3 | 156 | 0.65 | 0.86 | 31 | PLP |
| 4 | 85 | 0.38 | 0.76 | 21 | empty |
| 5 | 61 | 0.37 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 342 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6XWB · Crystal structure of an R-selective transaminase from Thermomyces stellatus. · 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
- Elsewhere: RCSB PDB 6XWB · PDBe 6XWB
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