Research workbench
Structure of ndpk H122G and tenofovir-diphosphate
Analyse Structure of ndpk H122G and tenofovir-diphosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FKB
- Type
- protein
- Length
- 898 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase, cytosolic
- EC
- 2.7.4.6
- UniProt
- P22887
- Ligands
- TNM, TNV, MG
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Nucleoside diphosphate kinase, cytosolic (EC 2.7.4.6) | protein | 150 | 43% helix, 17% strand | P22887 |
| D, E | Nucleoside diphosphate kinase, cytosolic (EC 2.7.4.6) | protein | 149 | 44% helix, 17% strand | P22887 |
Ligands and binding sites
- TNM · [(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-phosphonooxy-phosphinic acid · ligand · 5 copies · chains A, B, C, D, E, F
- TNV · [2-(6-amino-9H-purin-9-yl)-1-methylethoxy]methyl-triphosphate · ligand · chains D, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, D, B, E, F
- GOL · Glycerol · additive · 2 copies · chains C, D, 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 | 794 | 0.82 | 0.85 | 72 | empty |
| 2 | 587 | 0.80 | 0.86 | 60 | EDO |
| 3 | 704 | 0.80 | 0.84 | 67 | EDO |
| 4 | 571 | 0.79 | 0.85 | 63 | empty |
| 5 | 232 | 0.59 | 0.80 | 32 | TNM, MG |
Interfaces
9 interfaces between chains.
- A–C · 785 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 779 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 774 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 769 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 764 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3FKB · Structure of NDPK H122G and tenofovir-diphosphate · the same entry in another collection · chain F against F, 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 3FKB · PDBe 3FKB · UniProt P22887
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