MolNFT v1 · #90460 · protein
The structure of nucleoside diphosphate kinase (ndk) from burkholderia thailandensis bound to deoxyadenosine monophosphate
4EK2: “The structure of nucleoside diphosphate kinase (ndk) from burkholderia thailandensis bound to deoxyadenosine…”. X-ray diffraction, 2 ligands (DA, CL), 2 pockets (best druggability 0.54). MolNFT v1 #90460 on GenesisL1: 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
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