Research workbench
Crystal structure of chaetomium thermophilum glycerol kinase in complex with glycerol in P21212 space group
Analyse Crystal structure of chaetomium thermophilum glycerol kinase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZQ6
- Type
- protein
- Length
- 2,038 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase-like protein
- UniProt
- G0SAG9
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol kinase-like protein | protein | 510 | 38% helix, 22% strand | G0SAG9 |
| B | Glycerol kinase-like protein | protein | 510 | 37% helix, 22% strand | G0SAG9 |
| C, D | Glycerol kinase-like protein | protein | 509 | 38% helix, 21% strand | G0SAG9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.79 | 0.81 | 98 | GOL |
| 2 | 933 | 0.77 | 0.80 | 97 | GOL |
| 3 | 935 | 0.75 | 0.79 | 60 | empty |
| 4 | 564 | 0.70 | 0.79 | 49 | GOL |
| 5 | 527 | 0.69 | 0.79 | 54 | GOL |
Interfaces
5 interfaces between chains.
- B–C · 383 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 289 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 254 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 248 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 240 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ZQ6 · Crystal structure of Chaetomium thermophilum Glycerol Kinase in complex with glycerol in… · 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 G0SAG9
- Elsewhere: RCSB PDB 6ZQ6 · PDBe 6ZQ6 · UniProt G0SAG9
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