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Structure of the H122G nucleoside diphosphate kinase / D4T- TRIPHOSPHATE.MG complex
Analyse Structure of the H122G nucleoside diphosphate kinase / D4T- TRIPHOSPHATE.MG… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F3F
- Type
- protein
- Length
- 450 residues
- Chains
- 3
- 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
- D4T, D4D, MG, PO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein (nucleoside diphosphate kinase) (EC 2.7.4.6) | protein | 150 | 43% helix, 17% strand | P22887 |
Ligands and binding sites
- D4T · 2',3'-dehydro-2',3'-deoxy-thymidine 5'-triphosphate · ligand · 3 copies · chains A, B, C
- D4D · 2',3'-dehydro-2',3'-deoxy-thymidine 5'-diphosphate · ligand · chains B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.67 | 0.81 | 36 | empty |
| 2 | 157 | 0.51 | 0.79 | 25 | MG, D4T |
| 3 | 153 | 0.51 | 0.79 | 29 | PO4, MG, D4T, D4D |
| 4 | 146 | 0.48 | 0.78 | 23 | MG, D4T |
Interfaces
3 interfaces between chains.
- A–B · 770 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 766 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 738 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1F3F · Structure of the H122G nucleoside diphosphate kinase / D4T-TRIPHOSPHATE.MG complex · the same entry in another collection · chain A against A, 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 1F3F · PDBe 1F3F · UniProt P22887
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