Research workbench
Cryo-EM structure of plasmodium vivax hexokinase (closed state)
Analyse Cryo-EM structure of plasmodium vivax hexokinase (closed state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VYG
- Type
- protein
- Length
- 1,732 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotransferase
- EC
- 2.7.1.-
- UniProt
- A0A1G4HFC9
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphotransferase (EC 2.7.1.-) | protein | 433 | 43% helix, 13% strand | A0A1G4HFC9 |
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 | 896 | 0.84 | 0.86 | 79 | empty |
| 2 | 850 | 0.84 | 0.86 | 75 | empty |
| 3 | 1095 | 0.79 | 0.81 | 116 | empty |
| 4 | 524 | 0.77 | 0.84 | 54 | empty |
| 5 | 67 | 0.71 | 0.96 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 889 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 879 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 744 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 741 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 269 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6VYG · Cryo-EM structure of Plasmodium vivax hexokinase (Closed state) · 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 A0A1G4HFC9
- Elsewhere: RCSB PDB 6VYG · PDBe 6VYG · UniProt A0A1G4HFC9
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