Research workbench
Structure of DELTA4-dgka with amppcp in 9.9 mag
Analyse Structure of DELTA4-dgka with amppcp in 9.9 mag in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UXX
- Type
- protein
- Length
- 335 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diacylglycerol kinase
- EC
- 2.7.1.107
- UniProt
- P0ABN1
- Ligands
- ACP, NA, ZN, CL
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diacylglycerol kinase (EC 2.7.1.107) | protein | 114 | 89% helix, 0% strand | P0ABN1 |
| B | Diacylglycerol kinase (EC 2.7.1.107) | protein | 116 | 87% helix, 0% strand | P0ABN1 |
| C | Diacylglycerol kinase (EC 2.7.1.107) | protein | 105 | 87% helix, 0% strand | P0ABN1 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 2 copies · chains C
- CL · Chloride ion · ion · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 6 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.82 | 0.99 | 25 | empty |
| 2 | 305 | 0.55 | 0.75 | 31 | ZN, ACP, OLC |
| 3 | 225 | 0.54 | 0.77 | 31 | OLC, NA |
| 4 | 115 | 0.48 | 0.80 | 20 | MPD |
| 5 | 107 | 0.40 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1412 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1407 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1387 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4UXX · Structure of delta4-DgkA with AMPPCP in 9.9 MAG · 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 P0ABN1
- Elsewhere: RCSB PDB 4UXX · PDBe 4UXX · UniProt P0ABN1
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