Research workbench
Crystal structure of toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3 (NTPDASE3)
Analyse Crystal structure of toxoplasma gondii nucleoside triphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A57
- Type
- protein
- Length
- 2,374 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside-triphosphatase 1
- EC
- 3.6.1.15
- UniProt
- Q27893
- Ligands
- CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside-triphosphatase 1 (EC 3.6.1.15) | protein | 594 | 39% helix, 20% strand | Q27893 |
| C | Nucleoside-triphosphatase 1 (EC 3.6.1.15) | protein | 591 | 40% helix, 21% strand | Q27893 |
| D | Nucleoside-triphosphatase 1 (EC 3.6.1.15) | protein | 595 | 40% helix, 20% strand | Q27893 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.82 | 0.85 | 95 | empty |
| 2 | 1124 | 0.80 | 0.81 | 112 | empty |
| 3 | 716 | 0.79 | 0.84 | 73 | empty |
| 4 | 996 | 0.79 | 0.81 | 101 | empty |
| 5 | 80 | 0.75 | 0.98 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2515 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2452 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1259 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1232 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 397 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide (disulfide).
Compared structures
- 4A57 · Crystal structure of toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3… · the same entry in another collection · chain D against D, TM-score 1.00
- Q27893 · AlphaFold monomer V2.0 prediction for nucleoside-triphosphatase 1 (Q27893) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q27893
- Elsewhere: RCSB PDB 4A57 · PDBe 4A57 · UniProt Q27893
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.