MolNFT v1 · #87055 · protein
Structure determination of an integral membrane kinase
4BPD · Diacylglycerol kinase: “Structure determination of an integral membrane kinase”. X-ray diffraction, 2 ligands (78M, ZN), 12 pockets (best druggability 0.82). MolNFT v1 #87055 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4BPD
- Type
- protein
- Length
- 599 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
- 78M, ZN
- Pockets
- 12 · best druggability 0.82
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 | 118 | 88% helix, 0% strand | P0ABN1 |
| B | Diacylglycerol kinase (EC 2.7.1.107) | protein | 99 | 84% helix, 0% strand | P0ABN1 |
| C | Diacylglycerol kinase (EC 2.7.1.107) | protein | 93 | 87% helix, 0% strand | P0ABN1 |
| D | Diacylglycerol kinase (EC 2.7.1.107) | protein | 108 | 84% helix, 0% strand | P0ABN1 |
| E | Diacylglycerol kinase (EC 2.7.1.107) | protein | 89 | 88% helix, 0% strand | P0ABN1 |
| F | Diacylglycerol kinase (EC 2.7.1.107) | protein | 92 | 87% helix, 0% strand | P0ABN1 |
Ligands and binding sites
- 78M · (2S)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.82 | 0.98 | 25 | empty |
| 2 | 158 | 0.82 | 0.97 | 21 | empty |
| 3 | 332 | 0.69 | 0.82 | 26 | empty |
| 4 | 439 | 0.62 | 0.76 | 38 | empty |
| 5 | 186 | 0.55 | 0.79 | 20 | 78M |
Interfaces
8 interfaces between chains.
- D–E · 1432 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1416 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 1198 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 1136 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 1062 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 4BPD · PDBe 4BPD · UniProt P0ABN1
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