Research workbench
3'-fluoro-uridine diphosphate binding to nucleoside diphosphate kinase
Analyse 3'-fluoro-uridine diphosphate binding to nucleoside diphosphate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B99
- Type
- protein
- Length
- 900 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (nucleoside diphosphate kinase)
- EC
- 2.7.4.6
- UniProt
- P22887
- Ligands
- POP, FUP
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Protein (nucleoside diphosphate kinase) (EC 2.7.4.6) | protein | 150 | 43% helix, 16% strand | P22887 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 5 copies · chains B, C, D, E, F
- FUP · 2',3'-dideoxy-3'-fluoro-urididine-5'-diphosphate · ligand · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.78 | 0.85 | 55 | empty |
| 2 | 702 | 0.78 | 0.83 | 66 | empty |
| 3 | 391 | 0.77 | 0.86 | 52 | empty |
| 4 | 229 | 0.71 | 0.86 | 34 | empty |
| 5 | 194 | 0.69 | 0.87 | 35 | empty |
Interfaces
9 interfaces between chains.
- A–F · 792 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 770 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 769 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 768 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 760 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1B99 · 3'-fluoro-uridine diphosphate binding to nucleoside diphosphate kinase · the same entry in another collection · chain D against D, TM-score 1.00
- P22887 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase, cytosolic (P22887) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P22887
- Elsewhere: RCSB PDB 1B99 · PDBe 1B99 · UniProt P22887
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