Research workbench
2.4 ångström resolution crystal structure of putative nucleoside diphosphate kinase from toxoplasma gondii.
Analyse 2.4 ångström resolution crystal structure of putative nucleoside diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O0N
- Type
- protein
- Length
- 1,839 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- S8FF85
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H, I, J, K, L | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 153 | 47% helix, 16% strand | S8FF85 |
| B, D, E, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 154 | 49% helix, 16% strand | S8FF85 |
| G | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 152 | 47% helix, 16% strand | S8FF85 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.86 | 0.88 | 96 | empty |
| 2 | 438 | 0.83 | 0.90 | 54 | empty |
| 3 | 379 | 0.83 | 0.92 | 62 | empty |
| 4 | 379 | 0.83 | 0.91 | 58 | empty |
| 5 | 336 | 0.82 | 0.92 | 55 | empty |
Interfaces
27 interfaces between chains.
- H–J · 1066 Ų buried · 23 hydrogen bonds · protein-protein
- B–F · 1063 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1057 Ų buried · 22 hydrogen bonds · protein-protein
- I–L · 1054 Ų buried · 22 hydrogen bonds · protein-protein
- G–K · 1041 Ų buried · 20 hydrogen bonds · protein-protein
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 S8FF85
- Elsewhere: RCSB PDB 4O0N · PDBe 4O0N · UniProt S8FF85
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