Research workbench
Crystal structure of a hyperactive escherichia COLI glycerol kinase mutant GLY230 --> asp obtained using microfluidic crystallization devices
Analyse Crystal structure of a hyperactive escherichia COLI glycerol kinase mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EZW
- Type
- protein
- Length
- 3,939 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- P0A6F3
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol kinase (EC 2.7.1.30) | protein | 498 | 36% helix, 24% strand | P0A6F3 |
| B | Glycerol kinase (EC 2.7.1.30) | protein | 496 | 35% helix, 25% strand | P0A6F3 |
| E | Glycerol kinase (EC 2.7.1.30) | protein | 492 | 37% helix, 25% strand | P0A6F3 |
| G | Glycerol kinase (EC 2.7.1.30) | protein | 498 | 37% helix, 25% strand | P0A6F3 |
| C | Glycerol kinase (EC 2.7.1.30) | protein | 489 | 37% helix, 25% strand | P0A6F3 |
| D | Glycerol kinase (EC 2.7.1.30) | protein | 482 | 38% helix, 25% strand | P0A6F3 |
| F | Glycerol kinase (EC 2.7.1.30) | protein | 492 | 37% helix, 25% strand | P0A6F3 |
| H | Glycerol kinase (EC 2.7.1.30) | protein | 492 | 37% helix, 25% strand | P0A6F3 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, G
- CL · Chloride ion · ion · 8 copies · chains A, B, E, G, C, D, F, H
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, E, G, C, D, F, H
- GOL · Glycerol · additive · 8 copies · chains A, B, E, G, C, D, F, 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 | 888 | 0.78 | 0.81 | 60 | empty |
| 2 | 558 | 0.76 | 0.83 | 58 | CL |
| 3 | 835 | 0.74 | 0.78 | 86 | GOL |
| 4 | 779 | 0.73 | 0.78 | 83 | GOL |
| 5 | 331 | 0.73 | 0.85 | 46 | GOL |
Interfaces
13 interfaces between chains.
- B–G · 1678 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 1654 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1599 Ų buried · 26 hydrogen bonds · protein-protein
- C–H · 1520 Ų buried · 24 hydrogen bonds · protein-protein
- A–G · 868 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3EZW · Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp… · the same entry in another collection · chain H against H, TM-score 1.00
- P0A6F3 · AlphaFold monomer V2.0 prediction for glycerol kinase (P0A6F3) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P0A6F3
- Elsewhere: RCSB PDB 3EZW · PDBe 3EZW · UniProt P0A6F3
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