MolNFT v1 · #51744 · protein
Human erythrocyte pyruvate kinase: R486W mutant
2VGI · Pyruvate kinase isozymes R/L: “Human erythrocyte pyruvate kinase: R486W mutant”. X-ray diffraction, 4 ligands (FBP, PGA, K), 20 pockets (best druggability 0.88). MolNFT v1 #51744 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2VGI
- Type
- protein
- Length
- 2,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase isozymes R/L
- EC
- 2.7.1.40
- UniProt
- P30613
- Ligands
- FBP, PGA, K, MN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase isozymes R/L (EC 2.7.1.40) | protein | 517 | 39% helix, 21% strand | P30613 |
| B | Pyruvate kinase isozymes R/L (EC 2.7.1.40) | protein | 463 | 44% helix, 17% strand | P30613 |
| C | Pyruvate kinase isozymes R/L (EC 2.7.1.40) | protein | 515 | 39% helix, 21% strand | P30613 |
| D | Pyruvate kinase isozymes R/L (EC 2.7.1.40) | protein | 513 | 40% helix, 21% strand | P30613 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- PGA · 2-phosphoglycolic acid · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.88 | 0.89 | 136 | empty |
| 2 | 879 | 0.87 | 0.89 | 99 | empty |
| 3 | 580 | 0.82 | 0.88 | 45 | empty |
| 4 | 414 | 0.78 | 0.87 | 52 | empty |
| 5 | 817 | 0.77 | 0.81 | 75 | PGA, K |
Interfaces
6 interfaces between chains.
- A–C · 2999 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 2970 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1556 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1550 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2VGI · Human erythrocyte pyruvate kinase: R486W mutant · 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 P30613
- Elsewhere: RCSB PDB 2VGI · PDBe 2VGI · UniProt P30613
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