Research workbench
Crystal structure of the integral membrane enzyme dgka-ref, delta 7
Analyse Crystal structure of the integral membrane enzyme dgka-ref, delta 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BRB
- Type
- protein
- Length
- 593 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diacylglycerol kinase
- EC
- 2.7.1.107
- UniProt
- P0ABN1
- Ligands
- 78N, ZN
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diacylglycerol kinase (EC 2.7.1.107) | protein | 115 | 89% helix, 0% strand | P0ABN1 |
| B | Diacylglycerol kinase (EC 2.7.1.107) | protein | 99 | 87% helix, 0% strand | P0ABN1 |
| C | Diacylglycerol kinase (EC 2.7.1.107) | protein | 93 | 86% helix, 0% strand | P0ABN1 |
| D | Diacylglycerol kinase (EC 2.7.1.107) | protein | 108 | 87% helix, 0% strand | P0ABN1 |
| E | Diacylglycerol kinase (EC 2.7.1.107) | protein | 86 | 84% helix, 0% strand | P0ABN1 |
| F | Diacylglycerol kinase (EC 2.7.1.107) | protein | 92 | 87% helix, 0% strand | P0ABN1 |
Ligands and binding sites
- 78N · (2R)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 10 copies · chains A, B, C, D
- ZN · Zinc ion · metal · chains D
- FLC · Citrate anion · additive · chains D
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.82 | 0.98 | 23 | empty |
| 2 | 159 | 0.81 | 0.97 | 25 | empty |
| 3 | 561 | 0.73 | 0.80 | 42 | 78N |
| 4 | 320 | 0.57 | 0.76 | 34 | 78N |
| 5 | 125 | 0.44 | 0.76 | 15 | 78N |
Interfaces
8 interfaces between chains.
- A–B · 1374 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 1331 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1238 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 1149 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 1025 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4BRB · Crystal structure of the integral membrane enzyme DgkA-ref, delta 7 · 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 4BRB · PDBe 4BRB · UniProt P0ABN1
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