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Crystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti
Analyse Crystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NUG
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.788
- Source
- Mesorhizobium loti
- Molecule
- 3-oxoacyl-(Acyl-carrier protein) reductase
- EC
- 1.1.1.107
- UniProt
- Q988B7
- Ligands
- NAD
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.788 · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-oxoacyl-(Acyl-carrier protein) reductase (EC 1.1.1.107) | protein | 247 | 52% helix, 14% strand | Q988B7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.85 | 0.91 | 71 | NAD |
| 2 | 216 | 0.75 | 0.90 | 34 | NAD |
| 3 | 199 | 0.75 | 0.90 | 34 | NAD |
| 4 | 158 | 0.73 | 0.91 | 30 | NAD |
| 5 | 53 | 0.30 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1785 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1781 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1642 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1641 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 207 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3NUG · Crystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from mesorhizobium… · 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 3NUG · PDBe 3NUG · UniProt Q988B7
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