Research workbench
Crystal structure of trypanosoma cruzi pyruvate KINASE(TCPYK)IN complex with ponceau S.
Analyse Crystal structure of trypanosoma cruzi pyruvate KINASE(TCPYK)IN complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QV9
- Type
- protein
- Length
- 893 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase 2
- EC
- 2.7.1.40
- UniProt
- Q4D9Z4
- Ligands
- QV7, K, PO4
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase 2 (EC 2.7.1.40) | protein | 499 | 41% helix, 22% strand | Q4D9Z4 |
| B | Pyruvate kinase 2 (EC 2.7.1.40) | protein | 394 | 49% helix, 16% strand | Q4D9Z4 |
Ligands and binding sites
- QV7 · 3-hydroxy-4-[(E)-{2-sulfo-4-[(E)-(4-sulfophenyl)diazenyl]phenyl}diazenyl]naphthalene-2,7-disulfonic acid · ligand · chains B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.83 | 0.90 | 52 | empty |
| 2 | 533 | 0.66 | 0.77 | 52 | K, PO4 |
| 3 | 290 | 0.58 | 0.77 | 25 | empty |
| 4 | 276 | 0.56 | 0.77 | 24 | empty |
| 5 | 280 | 0.52 | 0.75 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 2262 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3QV9 · Crystal structure of Trypanosoma cruzi pyruvate kinase(TcPYK)in complex with ponceau S. · 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 Q4D9Z4
- Elsewhere: RCSB PDB 3QV9 · PDBe 3QV9 · UniProt Q4D9Z4
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