Research workbench
Structure of the nucleoside diphosphate KINASE/ALPHA-BORANO(RP)-TDP.MG complex
Analyse Structure of the nucleoside diphosphate KINASE/ALPHA-BORANO(RP)-TDP.MG complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F6T
- Type
- protein
- Length
- 451 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
- TBD, MG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (nucleoside diphosphate kinase) (EC 2.7.4.6) | protein | 150 | 43% helix, 17% strand | P22887 |
| B | Protein (nucleoside diphosphate kinase) (EC 2.7.4.6) | protein | 151 | 43% helix, 17% strand | P22887 |
Ligands and binding sites
- TBD · 2*-deoxy-thymidine-5*-alpha borano diphosphate (isomer rp) · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
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 | 332 | 0.65 | 0.80 | 36 | empty |
| 2 | 155 | 0.52 | 0.79 | 33 | MG, TBD |
| 3 | 162 | 0.52 | 0.79 | 29 | MG, TBD |
| 4 | 135 | 0.47 | 0.78 | 24 | MG, TBD |
Interfaces
3 interfaces between chains.
- A–C · 783 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 774 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 749 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1F6T · Structure of the nucleoside diphosphate KINASE/ALPHA-BORANO(RP)-TDP.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 1F6T · PDBe 1F6T · UniProt P22887
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