Research workbench
Crystal structure of complex of 4PAL (4-pyridoxolactone) and pldh (tetrameric pyridoxal 4-dehydrogenase) from mesorhizobium loti
Analyse Crystal structure of complex of 4PAL (4-pyridoxolactone) and pldh (tetrameric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RWB
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal 4-dehydrogenase
- EC
- 1.1.1.107
- UniProt
- Q988B7
- Ligands
- NAD, 4PL
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyridoxal 4-dehydrogenase (EC 1.1.1.107) | protein | 247 | 52% helix, 15% strand | Q988B7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- 4PL · 7-hydroxy-6-methylfuro[3,4-c]pyridin-1(3H)-one · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.86 | 0.91 | 75 | NAD, 4PL, GOL |
| 2 | 193 | 0.76 | 0.91 | 30 | NAD, 4PL |
| 3 | 189 | 0.75 | 0.91 | 30 | NAD, 4PL |
| 4 | 182 | 0.74 | 0.91 | 33 | NAD, 4PL |
| 5 | 57 | 0.33 | 0.77 | 9 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1794 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 1787 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1644 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1641 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 220 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3RWB · Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH (tetrameric pyridoxal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q988B7 · AlphaFold monomer V2.0 prediction for pyridoxal 4-dehydrogenase (Q988B7) · a predicted model of the same protein · chain A 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 Q988B7
- Elsewhere: RCSB PDB 3RWB · PDBe 3RWB · UniProt Q988B7
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