MolNFT v1 · #76780 · protein
Crystal structure of leishmania mexicana pyruvate KINASE(LMPYK)IN complex with ponceau S and acid blue 25.
3QV7: “Crystal structure of leishmania mexicana pyruvate KINASE(LMPYK)IN complex with ponceau S and acid blue 25.”. X-ray diffraction, 4 ligands (QV7, QV8, K), 20 pockets (best druggability 0.79). MolNFT v1 #76780 on GenesisL1: 3D…
- PDB
- 3QV7
- Type
- protein
- Length
- 1,785 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q27686
- Ligands
- QV7, QV8, K, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 494 | 41% helix, 22% strand | Q27686 |
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 493 | 41% helix, 22% strand | Q27686 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 400 | 49% helix, 17% strand | Q27686 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 398 | 49% helix, 17% strand | Q27686 |
Ligands and binding sites
- QV7 · 3-hydroxy-4-[(E)-{2-sulfo-4-[(E)-(4-sulfophenyl)diazenyl]phenyl}diazenyl]naphthalene-2,7-disulfonic acid · ligand · 5 copies · chains D, A, B, C
- QV8 · 9,10-dioxo-4-(phenylamino)-9,10-dihydroanthracene-2-sulfonic acid · ligand · chains B
- K · Potassium ion · metal · 8 copies · chains D, A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains D, A, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.79 | 0.88 | 38 | empty |
| 2 | 361 | 0.78 | 0.88 | 36 | empty |
| 3 | 1002 | 0.74 | 0.77 | 104 | K |
| 4 | 534 | 0.68 | 0.78 | 56 | SO4, K |
| 5 | 227 | 0.58 | 0.79 | 31 | K |
Interfaces
4 interfaces between chains.
- B–C · 2289 Ų buried · 21 hydrogen bonds · protein-protein
- D–A · 2279 Ų buried · 21 hydrogen bonds · protein-protein
- D–B · 986 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 965 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3QV7 · Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with ponceau S… · the same entry in another collection · chain C against C, TM-score 1.00
- Q27686 · AlphaFold monomer V2.0 prediction for pyruvate kinase (Q27686) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q27686
- Elsewhere: RCSB PDB 3QV7 · PDBe 3QV7 · UniProt Q27686
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