Research workbench
Crystal structure of an omega-transaminase from sphaerobacter thermophilus
Analyse Crystal structure of an omega-transaminase from sphaerobacter thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K8H
- Type
- protein
- Length
- 879 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase class-III
- UniProt
- D1C218
- Ligands
- PLR
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase class-III | protein | 438 | 44% helix, 15% strand | D1C218 |
| B | Aminotransferase class-III | protein | 441 | 45% helix, 15% strand | D1C218 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.77 | 0.81 | 85 | PLR |
| 2 | 873 | 0.77 | 0.80 | 88 | PLR |
| 3 | 50 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 4736 Ų buried · 78 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6K8H · Crystal structure of an omega-transaminase from Sphaerobacter thermophilus · 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 D1C218
- Elsewhere: RCSB PDB 6K8H · PDBe 6K8H · UniProt D1C218
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.