MolNFT v1 · #182731 · protein
Structure of NAD kinase
7N29 · NAD kinase 2, mitochondrial: “Structure of NAD kinase”. X-ray diffraction, 1 ligand (NAD), 15 pockets (best druggability 0.59). MolNFT v1 #182731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7N29
- Type
- protein
- Length
- 1,340 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD kinase 2, mitochondrial
- EC
- 2.7.1.23
- UniProt
- Q4G0N4
- Ligands
- NAD
- Pockets
- 15 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD kinase 2, mitochondrial (EC 2.7.1.23) | protein | 330 | 32% helix, 31% strand | Q4G0N4 |
| B | NAD kinase 2, mitochondrial (EC 2.7.1.23) | protein | 350 | 31% helix, 29% strand | Q4G0N4 |
| C | NAD kinase 2, mitochondrial (EC 2.7.1.23) | protein | 342 | 31% helix, 31% strand | Q4G0N4 |
| D | NAD kinase 2, mitochondrial (EC 2.7.1.23) | protein | 318 | 32% helix, 31% strand | Q4G0N4 |
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
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.59 | 0.79 | 51 | NAD |
| 2 | 233 | 0.58 | 0.80 | 43 | empty |
| 3 | 161 | 0.54 | 0.80 | 30 | empty |
| 4 | 188 | 0.52 | 0.78 | 35 | empty |
| 5 | 127 | 0.50 | 0.80 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 309 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 229 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 1 covalent (engineered, covalent ligand).
Compared structures
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 Q4G0N4
- Elsewhere: RCSB PDB 7N29 · PDBe 7N29 · UniProt Q4G0N4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.