MolNFT v1 · #94250 · protein
Structure of nucleoside diphosphate kinase (ndk) from burkholderia thailandensis bound to ADP
4HR2: “Structure of nucleoside diphosphate kinase (ndk) from burkholderia thailandensis bound to ADP”. X-ray diffraction, 1 ligand (ADP), 2 pockets (best druggability 0.50). MolNFT v1 #94250 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4HR2
- 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
- ADP
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 142 | 43% helix, 21% strand | Q2SWE7 |
| B | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 140 | 44% helix, 19% strand | Q2SWE7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, 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 | 171 | 0.50 | 0.77 | 24 | ADP |
| 2 | 179 | 0.48 | 0.76 | 23 | ADP |
Interfaces
1 interface between chains.
- A–B · 973 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4HR2 · Structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to… · 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 0.98
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 4HR2 · PDBe 4HR2 · UniProt Q2SWE7
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