Research workbench
The crystal structure of a S-selective transaminase from bacillus megaterium
Analyse The crystal structure of a S-selective transaminase from bacillus megaterium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G0A
- Type
- protein
- Length
- 1,882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transaminase
- EC
- 2.6.1.-
- UniProt
- A0A0Q9UXH6
- Ligands
- PLP
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Transaminase (EC 2.6.1.-) | protein | 468 | 39% helix, 18% strand | A0A0Q9UXH6 |
| B, D | Transaminase (EC 2.6.1.-) | protein | 473 | 38% helix, 18% strand | A0A0Q9UXH6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, D
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 | 1084 | 0.88 | 0.89 | 165 | PG4 |
| 2 | 709 | 0.82 | 0.85 | 72 | PLP, 1PE, PEG |
| 3 | 697 | 0.82 | 0.85 | 73 | PLP, PG4 |
| 4 | 725 | 0.81 | 0.85 | 69 | PLP, 1PE |
| 5 | 669 | 0.80 | 0.84 | 72 | PLP, PG4 |
Interfaces
6 interfaces between chains.
- A–B · 6001 Ų buried · 101 hydrogen bonds · protein-protein
- C–D · 5957 Ų buried · 98 hydrogen bonds · protein-protein
- A–D · 1593 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1535 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 157 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5G0A · The crystal structure of a S-selective transaminase from Bacillus megaterium · 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 A0A0Q9UXH6
- Elsewhere: RCSB PDB 5G0A · PDBe 5G0A · UniProt A0A0Q9UXH6
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