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The crystal structure of a new transaminase from the marine bacterium virgibacillus
Analyse The crystal structure of a new transaminase from the marine bacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FYQ
- Type
- protein
- Length
- 443 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine transaminase
- EC
- 2.6.1.18
- Ligands
- PLP, CL
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amine transaminase (EC 2.6.1.18) | protein | 443 | 46% helix, 17% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
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 | 728 | 0.69 | 0.76 | 65 | PLP, EDO |
| 2 | 312 | 0.55 | 0.75 | 28 | empty |
| 3 | 61 | 0.29 | 0.74 | 22 | empty |
Compared structures
- 6FYQ · The crystal structure of a new transaminase from the marine bacterium Virgibacillus · 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 6FYQ · PDBe 6FYQ
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