MolNFT v1 · #2361 · protein
Crystal structures of escherichia COLI glycerol kinase and the mutant A65T in an inactive tetramer: conformational changes and implications for allosteric regulation
1BU6 · Protein (glycerol kinase): “Crystal structures of escherichia COLI glycerol kinase and the mutant A65T in an inactive tetramer…”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #2361 on GenesisL1…
- PDB
- 1BU6
- Type
- protein
- Length
- 1,992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (glycerol kinase)
- EC
- 2.7.1.30
- UniProt
- P0A6F3
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Protein (glycerol kinase) (EC 2.7.1.30) | protein | 497 | 36% helix, 24% strand | P0A6F3 |
| Y | Protein (glycerol kinase) (EC 2.7.1.30) | protein | 499 | 36% helix, 24% strand | P0A6F3 |
| Z, X | Protein (glycerol kinase) (EC 2.7.1.30) | protein | 498 | 36% helix, 23% strand | P0A6F3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains O, X, Y, Z
- GOL · Glycerol · additive · 4 copies · chains O, Y, Z, X
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 | 572 | 0.81 | 0.86 | 55 | empty |
| 2 | 570 | 0.79 | 0.85 | 51 | empty |
| 3 | 479 | 0.72 | 0.82 | 47 | SO4, GOL |
| 4 | 52 | 0.72 | 0.98 | 13 | empty |
| 5 | 471 | 0.71 | 0.81 | 52 | SO4, GOL |
Interfaces
6 interfaces between chains.
- Z–X · 1767 Ų buried · 27 hydrogen bonds · protein-protein
- O–Y · 1720 Ų buried · 26 hydrogen bonds · protein-protein
- O–X · 843 Ų buried · 15 hydrogen bonds · protein-protein
- Y–Z · 818 Ų buried · 18 hydrogen bonds · protein-protein
- Y–X · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1BU6 · Crystal structures of escherichia COLI glycerol kinase and the mutant A65T in an inactive… · the same entry in another collection · chain O against O, TM-score 1.00
- P0A6F3 · AlphaFold monomer V2.0 prediction for glycerol kinase (P0A6F3) · a predicted model of the same protein · chain Z 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 1BU6 · PDBe 1BU6 · UniProt P0A6F3
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