Research workbench
Crystal structure of the C258S/C268S variant of toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3 (NTPDASE3) in complex with magnesium and amppnp
Analyse Crystal structure of the C258S/C268S variant of toxoplasma gondii nucleoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A5A
- Type
- protein
- Length
- 2,360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside-triphosphatase 1
- EC
- 3.6.1.5
- UniProt
- Q27893
- Ligands
- ANP, MG
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside-triphosphatase 1 (EC 3.6.1.5) | protein | 591 | 40% helix, 20% strand | Q27893 |
| B | Nucleoside-triphosphatase 1 (EC 3.6.1.5) | protein | 585 | 40% helix, 22% strand | Q27893 |
| C | Nucleoside-triphosphatase 1 (EC 3.6.1.5) | protein | 592 | 41% helix, 22% strand | Q27893 |
| D | Nucleoside-triphosphatase 1 (EC 3.6.1.5) | protein | 592 | 41% helix, 22% strand | Q27893 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.85 | 0.89 | 108 | empty |
| 2 | 671 | 0.85 | 0.89 | 107 | empty |
| 3 | 697 | 0.73 | 0.79 | 72 | ANP, MG |
| 4 | 694 | 0.72 | 0.79 | 76 | ANP, MG |
| 5 | 669 | 0.71 | 0.79 | 71 | ANP, MG |
Interfaces
2 interfaces between chains.
- C–D · 1567 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1550 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4A5A · Crystal structure of the C258S/C268S variant of Toxoplasma gondii nucleoside triphosphate… · 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 B against A, TM-score 0.96
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 4A5A · PDBe 4A5A · UniProt Q27893
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.