Research workbench
Plasmodium falciparum Nucleoside diphosphate kinase B
Analyse Plasmodium falciparum Nucleoside diphosphate kinase B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XIQ
- Type
- protein
- Length
- 894 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.05
- Source
- Plasmodium falciparum
- Molecule
- Nucleoside diphosphate kinase B
- EC
- 2.7.4.6
- UniProt
- Q8ID43
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · resolution 3.05 · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nucleoside diphosphate kinase B (EC 2.7.4.6) | protein | 149 | 42% helix, 17% strand | Q8ID43 |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.86 | 0.87 | 64 | empty |
| 2 | 207 | 0.84 | 0.97 | 42 | empty |
| 3 | 199 | 0.84 | 0.97 | 41 | empty |
| 4 | 168 | 0.82 | 0.97 | 40 | empty |
| 5 | 361 | 0.63 | 0.78 | 41 | empty |
Interfaces
12 interfaces between chains.
- B–E · 1102 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1091 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1074 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 948 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 933 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1XIQ · Plasmodium falciparum nucleoside diphosphate kinase B · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8ID43
- Elsewhere: RCSB PDB 1XIQ · PDBe 1XIQ · UniProt Q8ID43
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