Research workbench
Crystal structure of toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3 (NTPDASE3) in complex with AMP
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
- 4A59
- Type
- protein
- Length
- 2,371 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
- AMP
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside-triphosphatase 1 (EC 3.6.1.5) | protein | 593 | 39% helix, 20% strand | Q27893 |
| B | Nucleoside-triphosphatase 1 (EC 3.6.1.5) | protein | 593 | 39% helix, 23% strand | Q27893 |
| C | Nucleoside-triphosphatase 1 (EC 3.6.1.5) | protein | 590 | 39% helix, 21% strand | Q27893 |
| D | Nucleoside-triphosphatase 1 (EC 3.6.1.5) | protein | 595 | 39% helix, 22% strand | Q27893 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 5 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.88 | 0.89 | 144 | empty |
| 2 | 984 | 0.82 | 0.84 | 106 | AMP |
| 3 | 693 | 0.78 | 0.82 | 88 | empty |
| 4 | 121 | 0.76 | 0.95 | 25 | empty |
| 5 | 75 | 0.74 | 0.98 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2530 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2396 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1138 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1106 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 363 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 4A59 · Crystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3… · the same entry in another collection · chain C against C, 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 0.98
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 4A59 · PDBe 4A59 · UniProt Q27893
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