MolNFT v1 · #31861 · protein
Crystal structure of acanthamoeba polyphaga mimivirus ndk, the first viral nucleoside diphosphate kinase
2B8P · Probable nucleoside diphosphate kinase: “Crystal structure of acanthamoeba polyphaga mimivirus ndk, the first viral nucleoside diphosphate kinase”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.49). MolNFT v1…
- PDB
- 2B8P
- Type
- protein
- Length
- 259 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q5UQL3
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 129 | 44% helix, 20% strand | Q5UQL3 |
| B | Probable nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 130 | 45% helix, 22% strand | Q5UQL3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.49 | 0.77 | 27 | SO4 |
| 2 | 59 | 0.27 | 0.73 | 16 | SO4 |
Interfaces
1 interface between chains.
- A–B · 777 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2B8P · Crystal structure of Acanthamoeba polyphaga mimivirus NDK, the first viral nucleoside… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5UQL3
- Elsewhere: RCSB PDB 2B8P · PDBe 2B8P · UniProt Q5UQL3
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