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Crystal structure of pyruvate kinase II (pyka) from pseudomonas aeruginosa in complex with sodium malonate, magnesium and glucose-6- phosphate
Analyse Crystal structure of pyruvate kinase II (pyka) from pseudomonas aeruginosa in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QXL
- Type
- protein
- Length
- 5,716 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- A0A069PYA5
- Ligands
- G6P, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, L | Pyruvate kinase (EC 2.7.1.40) | protein | 483 | 39% helix, 24% strand | A0A069PYA5 |
| J | Pyruvate kinase (EC 2.7.1.40) | protein | 404 | 45% helix, 17% strand | A0A069PYA5 |
| K | Pyruvate kinase (EC 2.7.1.40) | protein | 482 | 37% helix, 23% strand | A0A069PYA5 |
Ligands and binding sites
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MLI · Malonate ion · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · 3 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.81 | 0.82 | 105 | empty |
| 2 | 1190 | 0.81 | 0.82 | 140 | MG, MLI |
| 3 | 648 | 0.78 | 0.84 | 82 | MG, MLI |
| 4 | 656 | 0.77 | 0.82 | 78 | MG, MLI |
| 5 | 569 | 0.76 | 0.83 | 77 | MG, MLI |
Interfaces
17 interfaces between chains.
- C–K · 1532 Ų buried · 18 hydrogen bonds · protein-protein
- E–H · 1532 Ų buried · 14 hydrogen bonds · protein-protein
- A–G · 1517 Ų buried · 18 hydrogen bonds · protein-protein
- I–L · 1515 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1510 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6QXL · Crystal Structure of Pyruvate Kinase II (PykA) from Pseudomonas aeruginosa in complex… · 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 A0A069PYA5
- Elsewhere: RCSB PDB 6QXL · PDBe 6QXL · UniProt A0A069PYA5
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