Research workbench
The structure of nucleoside diphosphate kinase (ndk) from burkholderia thailandensis bound to deoxyadenosine monophosphate
Analyse The structure of nucleoside diphosphate kinase (ndk) from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EK2
- Type
- protein
- Length
- 282 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q2SWE7
- Ligands
- DA, CL
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 142 | 43% helix, 20% strand | Q2SWE7 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 140 | 44% helix, 17% strand | Q2SWE7 |
Ligands and binding sites
- DA · 2'-deoxyadenosine-5'-monophosphate · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.54 | 0.77 | 30 | CL |
| 2 | 190 | 0.49 | 0.76 | 28 | CL, EDO |
Interfaces
1 interface between chains.
- A–B · 956 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4EK2 · The structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2SWE7 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q2SWE7) · a predicted model of the same protein · chain B 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 Q2SWE7
- Elsewhere: RCSB PDB 4EK2 · PDBe 4EK2 · UniProt Q2SWE7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.