Research workbench
Crystal structure of diacylglycerol kinase dgkb in complex with ADP and mg
Analyse Crystal structure of diacylglycerol kinase dgkb in complex with ADP and mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QV7
- Type
- protein
- Length
- 303 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diacylglycerol kinase dgkb
- EC
- 2.7.1.107
- UniProt
- Q6GFF9
- Ligands
- ADP, MG
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diacylglycerol kinase dgkb (EC 2.7.1.107) | protein | 303 | 23% helix, 35% strand | Q6GFF9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.56 | 0.78 | 43 | ADP |
| 2 | 52 | 0.33 | 0.78 | 13 | empty |
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2QV7 · Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GFF9 · AlphaFold monomer V2.0 prediction for diacylglycerol kinase (Q6GFF9) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q6GFF9
- Elsewhere: RCSB PDB 2QV7 · PDBe 2QV7 · UniProt Q6GFF9
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