Research workbench
Crystal structure of nucleoside diphosphate kinase B from trypanosoma brucei bound to GTP
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
- 4FKY
- Type
- protein
- Length
- 457 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q381H3
- Ligands
- GDP, MG
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 152 | 45% helix, 17% strand | Q381H3 |
| C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 153 | 47% helix, 16% strand | Q381H3 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.58 | 0.88 | 22 | empty |
| 2 | 59 | 0.53 | 0.88 | 20 | empty |
| 3 | 211 | 0.52 | 0.77 | 33 | GDP, MG, MPD |
| 4 | 202 | 0.50 | 0.76 | 18 | empty |
| 5 | 173 | 0.49 | 0.77 | 29 | GDP, MG |
Interfaces
3 interfaces between chains.
- A–B · 1186 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 776 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FKY · Crystal structure of nucleoside diphosphate kinase B from Trypanosoma brucei bound to GTP · 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 4FKY · PDBe 4FKY · UniProt Q381H3
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