Research workbench
Twinned pyruvate kinase from E. COLI in the T-state
Analyse Twinned pyruvate kinase from E. COLI in the T-state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YNG
- Type
- protein
- Length
- 3,720 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase I
- EC
- 2.7.1.40
- UniProt
- P0AD62
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Pyruvate kinase I (EC 2.7.1.40) | protein | 465 | 38% helix, 23% strand | P0AD62 |
| B | Pyruvate kinase I (EC 2.7.1.40) | protein | 464 | 36% helix, 22% strand | P0AD62 |
| C | Pyruvate kinase I (EC 2.7.1.40) | protein | 467 | 38% helix, 23% strand | P0AD62 |
| D | Pyruvate kinase I (EC 2.7.1.40) | protein | 463 | 37% helix, 24% strand | P0AD62 |
| E | Pyruvate kinase I (EC 2.7.1.40) | protein | 470 | 37% helix, 21% strand | P0AD62 |
| G | Pyruvate kinase I (EC 2.7.1.40) | protein | 463 | 38% helix, 23% strand | P0AD62 |
| H | Pyruvate kinase I (EC 2.7.1.40) | protein | 463 | 37% helix, 23% strand | P0AD62 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
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 | 116 | 0.72 | 0.93 | 29 | empty |
| 2 | 80 | 0.72 | 0.96 | 26 | empty |
| 3 | 69 | 0.71 | 0.97 | 24 | empty |
| 4 | 655 | 0.69 | 0.77 | 72 | SO4 |
| 5 | 494 | 0.69 | 0.80 | 52 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1240 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1237 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1157 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1148 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1027 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 P0AD62
- Elsewhere: RCSB PDB 4YNG · PDBe 4YNG · UniProt P0AD62
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