Research workbench
Escherichia COLI glycerol kinase mutant with bound ATP analog showing substantial domain motion
Analyse Escherichia COLI glycerol kinase mutant with bound ATP analog showing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BWF
- Type
- protein
- Length
- 988 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- P0A6F3
- Ligands
- ATF, MG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, O | Glycerol kinase (EC 2.7.1.30) | protein | 494 | 36% helix, 24% strand | P0A6F3 |
Ligands and binding sites
- ATF · Phosphodifluoromethylphosphonic acid-adenylate ester · ligand · 2 copies · chains Y, O
- MG · Magnesium ion · metal · 2 copies · chains Y, O
- GOL · Glycerol · additive · 2 copies · chains Y, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.70 | 0.81 | 47 | MG, ATF, GOL |
| 2 | 466 | 0.69 | 0.80 | 49 | MG, ATF, GOL |
| 3 | 302 | 0.59 | 0.78 | 51 | empty |
| 4 | 206 | 0.50 | 0.76 | 31 | empty |
| 5 | 71 | 0.45 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- Y–O · 1662 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1BWF · Escherichia COLI glycerol kinase mutant with bound ATP analog showing substantial domain… · the same entry in another collection · chain Y against Y, TM-score 1.00
- P0A6F3 · AlphaFold monomer V2.0 prediction for glycerol kinase (P0A6F3) · a predicted model of the same protein · chain Y 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 1BWF · PDBe 1BWF · UniProt P0A6F3
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