Research workbench
Structure of ternary complex of cgas with dsdna and bound 5 -PPPG(2 ,5 )pg
Analyse Structure of ternary complex of cgas with dsdna and bound 5 -PPPG(2 ,5 )pg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K98
- Type
- protein + DNA
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic gmp-AMP synthase; DNA-F; DNA-R
- EC
- 2.7.7.-
- UniProt
- Q8C6L5
- Ligands
- GTP, G, MG, ZN
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic gmp-AMP synthase (EC 2.7.7.-) | protein | 354 | 44% helix, 19% strand | Q8C6L5 |
| D | DNA-F | dna | 15 | — | — |
| E | DNA-R | dna | 14 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- G · Guanosine-5'-monophosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.76 | 0.95 | 20 | empty |
| 2 | 820 | 0.73 | 0.78 | 66 | MG, GTP, G |
| 3 | 414 | 0.60 | 0.76 | 30 | empty |
| 4 | 507 | 0.59 | 0.74 | 29 | empty |
| 5 | 181 | 0.53 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- D–E · 659 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- A–D · 519 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–E · 315 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4K98 · Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppG(2 ,5 )pG · the same entry in another collection · chain A against A, TM-score 1.00
- Q8C6L5 · AlphaFold monomer V2.0 prediction for cyclic gmp-AMP synthase (Q8C6L5) · a predicted model of the same protein · 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 Q8C6L5
- Elsewhere: RCSB PDB 4K98 · PDBe 4K98 · UniProt Q8C6L5
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