Research workbench
1.7 ångström resolution crystal structure of putative nucleoside diphosphate kinase from toxoplasma gondii with tyrosine of tag bound to active site
Analyse 1.7 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
- 5BXI
- Type
- protein
- Length
- 1,830 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
- BCT
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, K, L | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 152 | 49% helix, 16% strand | S8FF85 |
| B, E, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 153 | 49% helix, 16% strand | S8FF85 |
| C | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 143 | 46% helix, 17% strand | S8FF85 |
| D, G | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 158 | 47% helix, 15% strand | S8FF85 |
| I, J | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 152 | 47% helix, 16% strand | S8FF85 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 6 copies · chains A, B, C, D, E, F, I
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.86 | 0.88 | 97 | BCT |
| 2 | 458 | 0.83 | 0.91 | 59 | empty |
| 3 | 456 | 0.83 | 0.90 | 57 | empty |
| 4 | 449 | 0.83 | 0.90 | 59 | empty |
| 5 | 463 | 0.82 | 0.89 | 58 | empty |
Interfaces
30 interfaces between chains.
- A–G · 1052 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1049 Ų buried · 24 hydrogen bonds · protein-protein
- I–L · 1047 Ų buried · 25 hydrogen bonds · protein-protein
- J–K · 1047 Ų buried · 22 hydrogen bonds · protein-protein
- D–H · 1047 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5BXI · 1.7 Angstrom Resolution Crystal Structure of Putative Nucleoside Diphosphate Kinase from… · 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 S8FF85
- Elsewhere: RCSB PDB 5BXI · PDBe 5BXI · UniProt S8FF85
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