Research workbench
Crystal structure of a NAD kinase from archaeoglobus fulgidus in complex with NAD
Analyse Crystal structure of a 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
- 1Z0Z
- 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
- NAD
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 37% 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 | 21% helix, 37% strand | O30297 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.87 | 0.92 | 63 | empty |
| 2 | 60 | 0.71 | 0.97 | 19 | empty |
| 3 | 405 | 0.69 | 0.81 | 37 | NAD |
| 4 | 65 | 0.69 | 0.96 | 19 | empty |
| 5 | 447 | 0.69 | 0.80 | 40 | NAD |
Interfaces
6 interfaces between chains.
- C–D · 1294 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1285 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1158 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1141 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 219 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Z0Z · Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with NAD · the same entry in another collection · chain D against D, 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 1Z0Z · PDBe 1Z0Z · UniProt O30297
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