MolNFT v1 · #114695 · protein
1.7 ångström resolution crystal structure of putative nucleoside diphosphate kinase from toxoplasma gondii with tyrosine of tag bound to active site
5BXI: “1.7 ångström resolution crystal structure of putative nucleoside diphosphate kinase from toxoplasma gondii…”. X-ray diffraction, 1 ligand (BCT), 20 pockets (best druggability 0.86). MolNFT v1 #114695 on GenesisL1: 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
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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