MolNFT v1 · #84230 · protein
Crystal structure of the integral membrane diacylglycerol kinase - DELTA4
3ZE5: “Crystal structure of the integral membrane diacylglycerol kinase - DELTA4”. X-ray diffraction, 10 pockets (best druggability 0.82). MolNFT v1 #84230 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZE5
- 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
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 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 | 116 | 85% helix, 0% strand | P0ABN1 |
| C | Diacylglycerol kinase (EC 2.7.1.107) | protein | 104 | 88% helix, 0% strand | P0ABN1 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.82 | 0.98 | 26 | empty |
| 2 | 267 | 0.52 | 0.75 | 34 | empty |
| 3 | 185 | 0.51 | 0.77 | 22 | empty |
| 4 | 51 | 0.49 | 0.86 | 12 | empty |
| 5 | 95 | 0.35 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1402 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1400 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1367 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3ZE5 · Crystal structure of the integral membrane diacylglycerol kinase - delta4 · 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 B against A, TM-score 0.95
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 3ZE5 · PDBe 3ZE5 · UniProt P0ABN1
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