Research workbench
Crystal structure of a rok family glucokinase from streptomyces griseus
Analyse Crystal structure of a rok family glucokinase from streptomyces griseus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VGK
- Type
- protein
- Length
- 2,485 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase
- EC
- 2.7.1.2
- UniProt
- B1VZT1
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Glucokinase (EC 2.7.1.2) | protein | 311 | 39% helix, 22% strand | B1VZT1 |
| B | Glucokinase (EC 2.7.1.2) | protein | 312 | 39% helix, 23% strand | B1VZT1 |
| C, E, F, H | Glucokinase (EC 2.7.1.2) | protein | 310 | 40% helix, 20% strand | B1VZT1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, F, B, E, H, C, G, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.81 | 0.83 | 133 | SO4 |
| 2 | 745 | 0.79 | 0.83 | 69 | empty |
| 3 | 842 | 0.79 | 0.82 | 72 | empty |
| 4 | 936 | 0.76 | 0.79 | 113 | SO4 |
| 5 | 749 | 0.74 | 0.79 | 98 | empty |
Interfaces
15 interfaces between chains.
- D–F · 1989 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 1967 Ų buried · 11 hydrogen bonds · protein-protein
- E–H · 1953 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1926 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 674 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3VGK · Crystal structure of a ROK family glucokinase from Streptomyces griseus · 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 B1VZT1
- Elsewhere: RCSB PDB 3VGK · PDBe 3VGK · UniProt B1VZT1
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