Research workbench
Crystal structure of glycerol kinase in complex with glycerol from sinorhizobium meliloti 1021
Analyse Crystal structure of glycerol kinase in complex with glycerol from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E1J
- Type
- protein
- Length
- 1,922 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- O86033
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol kinase (EC 2.7.1.30) | protein | 498 | 37% helix, 23% strand | O86033 |
| B | Glycerol kinase (EC 2.7.1.30) | protein | 484 | 38% helix, 25% strand | O86033 |
| C | Glycerol kinase (EC 2.7.1.30) | protein | 503 | 37% helix, 23% strand | O86033 |
| D | Glycerol kinase (EC 2.7.1.30) | protein | 437 | 32% helix, 21% strand | O86033 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.71 | 0.82 | 59 | empty |
| 2 | 579 | 0.68 | 0.78 | 69 | empty |
| 3 | 324 | 0.68 | 0.83 | 41 | GOL |
| 4 | 214 | 0.68 | 0.85 | 27 | empty |
| 5 | 180 | 0.68 | 0.87 | 26 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1349 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1174 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 923 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 modified (engineered).
Compared structures
- 4E1J · Crystal structure of glycerol kinase in complex with glycerol from Sinorhizobium meliloti… · the same entry in another collection · chain D against D, TM-score 1.00
- O86033 · AlphaFold monomer V2.0 prediction for glycerol kinase (O86033) · a predicted model of the same protein · chain B 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 O86033
- Elsewhere: RCSB PDB 4E1J · PDBe 4E1J · UniProt O86033
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