Research workbench
Crystal structure of pyruvate kinase from toxoplasma gondii, 55.M00007
Analyse Crystal structure of pyruvate kinase from toxoplasma gondii, 55.M00007 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EOE
- Type
- protein
- Length
- 1,812 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
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 472 | 38% helix, 22% strand | Q969A2 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 483 | 40% helix, 22% strand | Q969A2 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 475 | 40% helix, 22% strand | Q969A2 |
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 382 | 46% helix, 16% strand | Q969A2 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.75 | 0.78 | 115 | GOL |
| 2 | 909 | 0.73 | 0.78 | 104 | empty |
| 3 | 848 | 0.71 | 0.77 | 80 | empty |
| 4 | 679 | 0.67 | 0.76 | 65 | empty |
| 5 | 598 | 0.64 | 0.75 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1728 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1566 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 669 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 632 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3EOE · Crystal Structure of Pyruvate Kinase from toxoplasma gondii, 55.m00007 · 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 3EOE · PDBe 3EOE · UniProt Q969A2
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