Research workbench
Crystal structure of chaetomium thermophilum glycerol kinase in complex with substrate in P1 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
- 6ZQ4
- Type
- protein
- Length
- 4,084 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase-like protein
- UniProt
- G0SAG9
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol kinase-like protein | protein | 510 | 37% helix, 22% strand | G0SAG9 |
| B | Glycerol kinase-like protein | protein | 510 | 37% helix, 22% strand | G0SAG9 |
| C | Glycerol kinase-like protein | protein | 509 | 37% helix, 22% strand | G0SAG9 |
| D | Glycerol kinase-like protein | protein | 509 | 37% helix, 22% strand | G0SAG9 |
| E, H | Glycerol kinase-like protein | protein | 511 | 37% helix, 21% strand | G0SAG9 |
| F, G | Glycerol kinase-like protein | protein | 512 | 37% helix, 22% strand | G0SAG9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.80 | 0.81 | 77 | empty |
| 2 | 1043 | 0.79 | 0.80 | 93 | PO4, GOL |
| 3 | 1051 | 0.78 | 0.80 | 110 | GOL |
| 4 | 754 | 0.73 | 0.79 | 92 | empty |
| 5 | 555 | 0.71 | 0.80 | 57 | PO4, GOL |
Interfaces
12 interfaces between chains.
- B–C · 532 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 402 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 386 Ų buried · 2 hydrogen bonds · protein-protein
- C–H · 358 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 347 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6ZQ4 · Crystal structure of Chaetomium thermophilum Glycerol Kinase in complex with substrate in… · the same entry in another collection · chain H against H, 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 6ZQ4 · PDBe 6ZQ4 · UniProt G0SAG9
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