Research workbench
Crystal structure of nucleoside diphosphate kinase B from trypanosoma brucei, apo form
Analyse Crystal structure of nucleoside diphosphate kinase B from trypanosoma brucei… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F36
- Type
- protein
- Length
- 842 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q381H3
- Ligands
- SCN
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 141 | 46% helix, 18% strand | Q381H3 |
| C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 140 | 44% helix, 19% strand | Q381H3 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 140 | 44% helix, 19% strand | Q381H3 |
| D | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 138 | 43% helix, 19% strand | Q381H3 |
| E | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 147 | 44% helix, 18% strand | Q381H3 |
| F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 136 | 45% helix, 19% strand | Q381H3 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.83 | 0.91 | 75 | empty |
| 2 | 277 | 0.81 | 0.92 | 52 | empty |
| 3 | 217 | 0.79 | 0.93 | 39 | empty |
| 4 | 126 | 0.67 | 0.89 | 27 | empty |
| 5 | 64 | 0.54 | 0.87 | 22 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1181 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1178 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1154 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 728 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 714 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4F36 · Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, apo form · 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 Q381H3
- Elsewhere: RCSB PDB 4F36 · PDBe 4F36 · UniProt Q381H3
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