MolNFT v1 · #57695 · protein
Crystal structure of yeast NADH kinase complexed with NADH
3AFO · NADH kinase POS5: “Crystal structure of yeast NADH kinase complexed with NADH”. X-ray diffraction, 1 ligand (NAI), 9 pockets (best druggability 0.73). MolNFT v1 #57695 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3AFO
- Type
- protein
- Length
- 701 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH kinase POS5
- EC
- 2.7.1.86
- UniProt
- Q06892
- Ligands
- NAI
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH kinase POS5 (EC 2.7.1.86) | protein | 360 | 21% helix, 34% strand | Q06892 |
| B | NADH kinase POS5 (EC 2.7.1.86) | protein | 341 | 23% helix, 35% strand | Q06892 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.73 | 0.86 | 47 | MPD |
| 2 | 187 | 0.69 | 0.87 | 41 | MPD |
| 3 | 103 | 0.37 | 0.75 | 25 | empty |
| 4 | 107 | 0.36 | 0.74 | 19 | empty |
| 5 | 72 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2000 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3AFO · Crystal Structure of Yeast NADH Kinase complexed with NADH · the same entry in another collection · chain A against A, TM-score 1.00
- Q06892 · AlphaFold monomer V2.0 prediction for NADH kinase POS5, mitochondrial (Q06892) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q06892
- Elsewhere: RCSB PDB 3AFO · PDBe 3AFO · UniProt Q06892
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