MolNFT v1 · #88675 · protein
Crystal structure of an integral membrane kinase - V2.3
4D2E · Diacylglycerol kinase: “Crystal structure of an integral membrane kinase - V2.3”. X-ray diffraction, 4 ligands (78N, 78M, NA), 13 pockets (best druggability 0.82). MolNFT v1 #88675 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4D2E
- Type
- protein
- Length
- 597 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
- 13 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diacylglycerol kinase (EC 2.7.1.107) | protein | 116 | 87% helix, 0% strand | P0ABN1 |
| B | Diacylglycerol kinase (EC 2.7.1.107) | protein | 98 | 82% helix, 0% strand | P0ABN1 |
| C | Diacylglycerol kinase (EC 2.7.1.107) | protein | 93 | 85% 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 | 90 | 82% helix, 0% strand | P0ABN1 |
| F | Diacylglycerol kinase (EC 2.7.1.107) | protein | 92 | 85% helix, 0% strand | P0ABN1 |
Ligands and binding sites
- 78N · (2R)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 11 copies · chains A, B, C, D, E
- 78M · (2S)-2,3-dihydroxypropyl(7z)-pentadec-7-enoate · ligand · 7 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains D, F
- ZN · Zinc ion · metal · chains D
- FLC · Citrate anion · additive · 2 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.82 | 0.98 | 27 | empty |
| 2 | 136 | 0.81 | 0.98 | 23 | NA |
| 3 | 352 | 0.70 | 0.81 | 25 | 78M |
| 4 | 376 | 0.61 | 0.77 | 32 | 78N |
| 5 | 224 | 0.58 | 0.79 | 21 | 78N |
Interfaces
8 interfaces between chains.
- A–B · 1445 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 1360 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1227 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1187 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 1149 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4D2E · Crystal structure of an integral membrane kinase - v2.3 · 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 4D2E · PDBe 4D2E · UniProt P0ABN1
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