Research workbench
Crystal structure of escherichia COLI pyruvate kinase II
Analyse Crystal structure of escherichia COLI pyruvate kinase II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K0K
- Type
- protein
- Length
- 1,746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- C3T5U7
- Ligands
- MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 479 | 38% helix, 20% strand | C3T5U7 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 478 | 37% helix, 20% strand | C3T5U7 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 397 | 43% helix, 16% strand | C3T5U7 |
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 392 | 43% helix, 17% strand | C3T5U7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, D
- CIT · Citric acid · additive · 3 copies · chains A, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.77 | 0.81 | 81 | empty |
| 2 | 742 | 0.77 | 0.81 | 79 | empty |
| 3 | 428 | 0.64 | 0.78 | 48 | empty |
| 4 | 565 | 0.63 | 0.75 | 52 | empty |
| 5 | 157 | 0.61 | 0.84 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1287 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1082 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 77 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6K0K · Crystal structure of Escherichia coli pyruvate kinase II · the same entry in another collection · chain D against D, 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 C3T5U7
- Elsewhere: RCSB PDB 6K0K · PDBe 6K0K · UniProt C3T5U7
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