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Crystal structure of trypanosoma brucei gambiense glycerol kinase complex with ADP, MG2+, and glycerol
Analyse Crystal structure of trypanosoma brucei gambiense glycerol kinase complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WXL
- Type
- protein
- Length
- 2,052 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol kinase
- EC
- 2.7.1.30
- UniProt
- D3KVM3
- Ligands
- ADP, MG
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycerol kinase (EC 2.7.1.30) | protein | 513 | 37% helix, 25% strand | D3KVM3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.73 | 0.86 | 33 | empty |
| 2 | 764 | 0.71 | 0.77 | 72 | GOL |
| 3 | 675 | 0.70 | 0.78 | 63 | GOL, ADP |
| 4 | 522 | 0.70 | 0.79 | 58 | empty |
| 5 | 723 | 0.70 | 0.77 | 73 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1419 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1394 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3WXL · Crystal structure of trypanosoma brucei gambiense glycerol kinase complex with adp, mg2+… · 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 D3KVM3
- Elsewhere: RCSB PDB 3WXL · PDBe 3WXL · UniProt D3KVM3
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