MolNFT v1 · #117046 · protein
Diacylglycerol kinase solved by multi crystal multi orientation native sad
5DWK: “Diacylglycerol kinase solved by multi crystal multi orientation native sad”. X-ray diffraction, 4 ligands (78N, 78M, NA), 7 pockets (best druggability 0.81). MolNFT v1 #117046 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DWK
- Type
- protein
- Length
- 566 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, 78M, NA, ZN
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diacylglycerol kinase (EC 2.7.1.107) | protein | 95 | 81% helix, 0% strand | P0ABN1 |
| B | Diacylglycerol kinase (EC 2.7.1.107) | protein | 111 | 91% helix, 0% strand | P0ABN1 |
| C | Diacylglycerol kinase (EC 2.7.1.107) | protein | 106 | 88% helix, 0% strand | P0ABN1 |
| D | Diacylglycerol kinase (EC 2.7.1.107) | protein | 87 | 86% helix, 0% strand | P0ABN1 |
| E | Diacylglycerol kinase (EC 2.7.1.107) | protein | 84 | 83% helix, 0% strand | P0ABN1 |
| F | Diacylglycerol kinase (EC 2.7.1.107) | protein | 83 | 82% helix, 0% strand | P0ABN1 |
Ligands and binding sites
- 78N · (2R)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 7 copies · chains A, B, C, D
- 78M · (2S)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 6 copies · chains A, C, B, F, D
- NA · Sodium ion · metal · chains A, B
- ZN · Zinc ion · metal · chains C
- CIT · Citric acid · additive · chains C
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.81 | 0.98 | 23 | empty |
| 2 | 220 | 0.79 | 0.92 | 32 | NA |
| 3 | 512 | 0.71 | 0.80 | 40 | 78N, 78M |
| 4 | 271 | 0.51 | 0.74 | 33 | 78N |
| 5 | 121 | 0.43 | 0.76 | 15 | 78N |
Interfaces
8 interfaces between chains.
- A–B · 1337 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 1319 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1202 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 1124 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 1037 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DWK · Diacylglycerol Kinase solved by multi crystal multi orientation native SAD · 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 5DWK · PDBe 5DWK · UniProt P0ABN1
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