Research workbench
Crystal structure of pyruvate kinase (pyk) from plasmodium falciparum in complex with oxalate and ATP
Analyse Crystal structure of pyruvate kinase (pyk) from plasmodium falciparum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KSH
- Type
- protein
- Length
- 1,960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- C6KTA4
- Ligands
- ATP, OXL, MG, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyruvate kinase (EC 2.7.1.40) | protein | 490 | 40% helix, 23% strand | C6KTA4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- K · Potassium 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
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 | 1072 | 0.85 | 0.86 | 143 | MG, ATP, K, OXL |
| 2 | 937 | 0.84 | 0.86 | 130 | MG, ATP, K, OXL |
| 3 | 401 | 0.67 | 0.80 | 58 | empty |
| 4 | 364 | 0.66 | 0.80 | 49 | empty |
| 5 | 160 | 0.62 | 0.85 | 24 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2926 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2922 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 1002 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 998 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6KSH · Crystal structure of pyruvate kinase (PYK) from Plasmodium falciparum in complex with… · 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 C6KTA4
- Elsewhere: RCSB PDB 6KSH · PDBe 6KSH · UniProt C6KTA4
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