Research workbench
Crystal structure of ygjg in complex with pyridoxal-5'-phosphate and putrescine
Analyse Crystal structure of ygjg in complex with pyridoxal-5'-phosphate and putrescine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UOX
- Type
- protein
- Length
- 1,813 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putrescine aminotransferase
- EC
- 2.6.1.82
- UniProt
- P42588
- Ligands
- PLP, PUT
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putrescine aminotransferase (EC 2.6.1.82) | protein | 453 | 47% helix, 16% strand | P42588 |
| B, D | Putrescine aminotransferase (EC 2.6.1.82) | protein | 452 | 48% helix, 17% strand | P42588 |
| C | Putrescine aminotransferase (EC 2.6.1.82) | protein | 456 | 47% helix, 17% strand | P42588 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- PUT · 1,4-diaminobutane · ligand · 3 copies · chains A, B, C, D
- FMT · Formic acid · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.83 | 0.91 | 66 | PLP, PUT |
| 2 | 485 | 0.83 | 0.90 | 64 | PLP, PUT, FMT |
| 3 | 469 | 0.83 | 0.90 | 73 | PLP, PUT |
| 4 | 448 | 0.83 | 0.90 | 67 | PLP |
| 5 | 1155 | 0.82 | 0.84 | 79 | FMT, PEG |
Interfaces
4 interfaces between chains.
- A–B · 6323 Ų buried · 71 hydrogen bonds · protein-protein
- C–D · 6281 Ų buried · 67 hydrogen bonds · protein-protein
- B–C · 799 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 790 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4UOX · Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate and putrescine · the same entry in another collection · chain A against A, TM-score 1.00
- P42588 · AlphaFold monomer V2.0 prediction for putrescine aminotransferase (P42588) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P42588
- Elsewhere: RCSB PDB 4UOX · PDBe 4UOX · UniProt P42588
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