Research workbench
NMR solution structure of E. COLI diacylglycerol kinase (dagk) in dpc micelles
Analyse NMR solution structure of E. COLI diacylglycerol kinase (dagk) in dpc micelles in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KDC
- Type
- protein
- Length
- 363 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diacylglycerol kinase
- EC
- 2.7.1.107
- UniProt
- P0ABN1
- Pockets
- 8 · best druggability 0.86
Structure
solution nmr · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Diacylglycerol kinase (EC 2.7.1.107) | protein | 121 | 72% helix, 0% strand | P0ABN1 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.86 | 0.86 | 122 | empty |
| 2 | 56 | 0.61 | 0.92 | 12 | empty |
| 3 | 190 | 0.58 | 0.81 | 30 | empty |
| 4 | 183 | 0.58 | 0.81 | 27 | empty |
| 5 | 216 | 0.57 | 0.79 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1735 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1734 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1733 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2KDC · NMR Solution Structure of E. coli diacylglycerol kinase (DAGK) in DPC micelles · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABN1 · AlphaFold monomer V2.0 prediction for diacylglycerol kinase (P0ABN1) · a predicted model of the same protein · chain A against A, TM-score 0.29
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 P0ABN1
- Elsewhere: RCSB PDB 2KDC · PDBe 2KDC · UniProt P0ABN1
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