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Structure of DELTA7-dgka in 7.9 mag by serial femtosecond crystatallography to 2.18 ångström resolution
Analyse Structure of DELTA7-dgka in 7.9 mag by serial femtosecond crystatallography to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UYO
- Type
- protein
- Length
- 608 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diacylglycerol kinase-delta 7
- EC
- 2.7.1.107
- UniProt
- P0ABN1
- Ligands
- 79N, 79M, ZN
- Pockets
- 12 · 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-delta 7 (EC 2.7.1.107) | protein | 116 | 89% helix, 0% strand | P0ABN1 |
| B | Diacylglycerol kinase-delta 7 (EC 2.7.1.107) | protein | 98 | 85% helix, 0% strand | P0ABN1 |
| C | Diacylglycerol kinase-delta 7 (EC 2.7.1.107) | protein | 90 | 86% helix, 0% strand | P0ABN1 |
| D | Diacylglycerol kinase-delta 7 (EC 2.7.1.107) | protein | 108 | 87% helix, 0% strand | P0ABN1 |
| E | Diacylglycerol kinase-delta 7 (EC 2.7.1.107) | protein | 101 | 80% helix, 0% strand | P0ABN1 |
| F | Diacylglycerol kinase-delta 7 (EC 2.7.1.107) | protein | 95 | 83% helix, 0% strand | P0ABN1 |
Ligands and binding sites
- 79N · (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate · ligand · 5 copies · chains A, B, C, D
- 79M · (2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate · ligand · 4 copies · chains B, C, D, F
- ZN · Zinc ion · metal · chains D
- FLC · Citrate anion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.82 | 0.98 | 23 | empty |
| 2 | 141 | 0.82 | 0.98 | 23 | empty |
| 3 | 333 | 0.67 | 0.81 | 26 | 79N |
| 4 | 381 | 0.59 | 0.75 | 35 | 79N |
| 5 | 193 | 0.55 | 0.79 | 21 | 79M, 79N |
Interfaces
8 interfaces between chains.
- A–B · 1437 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1370 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1315 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1211 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 1172 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4UYO · Structure of delta7-DgkA in 7.9 MAG by serial femtosecond crystatallography to 2.18… · 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 4UYO · PDBe 4UYO · UniProt P0ABN1
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