MolNFT v1 · #107852 · protein
Crystal structure of ygjg in complex with pyridoxal-5'-phosphate
4UOY · Putrescine aminotransferase: “Crystal structure of ygjg in complex with pyridoxal-5'-phosphate”. X-ray diffraction, 1 ligand (PLP), 13 pockets (best druggability 0.84). MolNFT v1 #107852 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4UOY
- Type
- protein
- Length
- 1,810 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
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putrescine aminotransferase (EC 2.6.1.82) | protein | 454 | 48% helix, 18% strand | P42588 |
| B, C, D | Putrescine aminotransferase (EC 2.6.1.82) | protein | 452 | 48% helix, 18% strand | P42588 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
- FMT · Formic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.84 | 0.91 | 72 | PLP, GOL |
| 2 | 465 | 0.84 | 0.91 | 72 | PLP |
| 3 | 518 | 0.84 | 0.90 | 75 | PLP |
| 4 | 518 | 0.84 | 0.90 | 75 | FMT, PLP |
| 5 | 1142 | 0.83 | 0.84 | 78 | GOL |
Interfaces
4 interfaces between chains.
- C–D · 6322 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 6316 Ų buried · 70 hydrogen bonds · protein-protein
- B–C · 807 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 783 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4UOY · Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate · the same entry in another collection · chain B against B, TM-score 1.00
- P42588 · AlphaFold monomer V2.0 prediction for putrescine aminotransferase (P42588) · a predicted model of the same protein · chain B 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 4UOY · PDBe 4UOY · UniProt P42588
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