MolNFT v1 · #72610 · protein
Crystal structure of tetrameric pyridoxal 4-dehydrogenase from mesorhizobium loti
3NDR · 3-oxoacyl-(acyl-carrier protein) reductase: “Crystal structure of tetrameric pyridoxal 4-dehydrogenase from mesorhizobium loti”. X-ray diffraction, 1 ligand (NAD), 5 pockets (best druggability 0.88). MolNFT v1 #72610 on GenesisL1…
- PDB
- 3NDR
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-(acyl-carrier protein) reductase
- EC
- 1.1.1.107
- UniProt
- Q988B7
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 51% 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 | 51% helix, 14% strand | Q988B7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.88 | 0.89 | 119 | NAD |
| 2 | 216 | 0.74 | 0.89 | 35 | NAD |
| 3 | 220 | 0.73 | 0.88 | 34 | NAD |
| 4 | 66 | 0.27 | 0.73 | 15 | empty |
| 5 | 60 | 0.25 | 0.72 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1845 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1838 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1628 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1620 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 245 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3NDR · Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti · 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 3NDR · PDBe 3NDR · UniProt Q988B7
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