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The crystal structure of the K38A/K137A/K233A/K234A quadruple mutant of E. COLI yggs in complex with plp
Analyse The crystal structure of the K38A/K137A/K233A/K234A quadruple mutant of E. COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UB8
- Type
- protein
- Length
- 451 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal phosphate homeostasis protein
- UniProt
- C3SV52
- Ligands
- PLP
- Pockets
- 5 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal phosphate homeostasis protein | protein | 226 | 48% helix, 18% strand | C3SV52 |
| B | Pyridoxal phosphate homeostasis protein | protein | 225 | 50% helix, 18% strand | C3SV52 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- BU1 · 1,4-butanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.39 | 0.81 | 16 | empty |
| 2 | 81 | 0.38 | 0.77 | 16 | PLP |
| 3 | 59 | 0.32 | 0.76 | 16 | PLP |
| 4 | 57 | 0.30 | 0.75 | 14 | empty |
| 5 | 57 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 204 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7UB8 · The crystal structure of the K38A/K137A/K233A/K234A quadruple mutant of E. coli YGGS in… · 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 C3SV52
- Elsewhere: RCSB PDB 7UB8 · PDBe 7UB8 · UniProt C3SV52
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