Research workbench
Crystal structure of the toxoplasma gondii pyruvate kinase N terminal truncated
Analyse Crystal structure of the toxoplasma gondii pyruvate kinase N terminal truncated in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GG8
- Type
- protein
- Length
- 1,915 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q969A2
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 478 | 40% helix, 22% strand | Q969A2 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 463 | 40% helix, 21% strand | Q969A2 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 491 | 39% helix, 22% strand | Q969A2 |
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 483 | 40% helix, 22% strand | Q969A2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.80 | 0.82 | 86 | empty |
| 2 | 481 | 0.69 | 0.80 | 54 | empty |
| 3 | 520 | 0.69 | 0.79 | 51 | empty |
| 4 | 732 | 0.69 | 0.76 | 43 | empty |
| 5 | 411 | 0.66 | 0.79 | 48 | GOL |
Interfaces
4 interfaces between chains.
- A–C · 2082 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1802 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 784 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 750 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3GG8 · Crystal structure of the Toxoplasma gondii Pyruvate Kinase N terminal truncated · 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 Q969A2
- Elsewhere: RCSB PDB 3GG8 · PDBe 3GG8 · UniProt Q969A2
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