Research workbench
Crystal structure of NAD kinase from thermotoga maritima
Analyse Crystal structure of NAD kinase from thermotoga maritima in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YT5
- Type
- protein
- Length
- 1,020 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic POLYPHOSPHATE/ATP-NAD kinase
- EC
- 2.7.1.23
- UniProt
- Q9X255
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Inorganic POLYPHOSPHATE/ATP-NAD kinase (EC 2.7.1.23) | protein | 256 | 18% helix, 44% strand | Q9X255 |
| C | Inorganic POLYPHOSPHATE/ATP-NAD kinase (EC 2.7.1.23) | protein | 252 | 16% helix, 43% strand | Q9X255 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.80 | 0.81 | 111 | SO4 |
| 2 | 518 | 0.70 | 0.80 | 45 | SO4 |
| 3 | 619 | 0.70 | 0.78 | 55 | SO4 |
| 4 | 509 | 0.66 | 0.78 | 68 | empty |
| 5 | 137 | 0.64 | 0.87 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–C · 936 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 924 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 684 Ų buried · 4 hydrogen bonds · protein-protein
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 Q9X255
- Elsewhere: RCSB PDB 1YT5 · PDBe 1YT5 · UniProt Q9X255
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