Research workbench
Crystal structure of acanthamoeba polyphaga mimivirus ndk, the first viral nucleoside diphosphate kinase
Analyse Crystal structure of acanthamoeba polyphaga mimivirus ndk, the first viral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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