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Crystal structure of an NAD kinase from archaeoglobus fulgidus in complex with ATP
Analyse Crystal structure of an NAD kinase from archaeoglobus fulgidus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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