Research workbench
Nucleoside diphosphate kinase B from trypanosoma cruzi
Analyse Nucleoside diphosphate kinase B from trypanosoma cruzi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PRV
- Type
- protein
- Length
- 892 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
- Q4E256
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 150 | 46% helix, 16% strand | Q4E256 |
| B, C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 46% helix, 16% strand | Q4E256 |
| E | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 140 | 36% helix, 17% strand | Q4E256 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.84 | 0.92 | 57 | empty |
| 2 | 327 | 0.83 | 0.93 | 46 | empty |
| 3 | 305 | 0.83 | 0.93 | 47 | empty |
| 4 | 362 | 0.79 | 0.89 | 63 | empty |
| 5 | 189 | 0.52 | 0.78 | 25 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1130 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1120 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1116 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 774 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 752 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3PRV · Nucleoside diphosphate kinase B from Trypanosoma cruzi · 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 Q4E256
- Elsewhere: RCSB PDB 3PRV · PDBe 3PRV · UniProt Q4E256
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