MolNFT v1 · #29187 · protein
Crystal structure of an NAD kinase from archaeoglobus fulgidus in complex with ATP
1Z0S · Probable inorganic POLYPHOSPHATE/ATP-NAD kinase: “Crystal structure of an NAD kinase from archaeoglobus fulgidus in complex with ATP”. X-ray diffraction, 3 ligands (ATP, POP, MG), 11 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 1Z0S
- Type
- protein
- Length
- 996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable inorganic POLYPHOSPHATE/ATP-NAD kinase
- EC
- 2.7.1.23
- UniProt
- O30297
- Ligands
- ATP, POP, MG
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Probable inorganic POLYPHOSPHATE/ATP-NAD kinase (EC 2.7.1.23) | protein | 249 | 20% helix, 43% strand | O30297 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, B, C
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.86 | 0.91 | 64 | empty |
| 2 | 377 | 0.75 | 0.85 | 43 | MG, ATP, POP |
| 3 | 391 | 0.74 | 0.85 | 46 | MG, ATP, POP |
| 4 | 446 | 0.74 | 0.84 | 50 | MG, ATP, POP |
| 5 | 420 | 0.73 | 0.83 | 50 | MG, ATP, POP |
Interfaces
6 interfaces between chains.
- A–D · 1225 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1212 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1211 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1196 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 217 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Z0S · Crystal structure of an NAD kinase from Archaeoglobus fulgidus in complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- O30297 · AlphaFold monomer V2.0 prediction for NAD kinase (O30297) · 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 O30297
- Elsewhere: RCSB PDB 1Z0S · PDBe 1Z0S · UniProt O30297
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