Research workbench
Structure of ternary complex of cgas with dsdna and bound 5 -PPPDG(2 , 5 )pdg
Analyse Structure of ternary complex of cgas with dsdna and bound 5 -PPPDG(2 , 5 )pdg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K99
- 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
- GH3, GDO, MG, ZN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic gmp-AMP synthase (EC 2.7.7.-) | protein | 354 | 45% helix, 19% strand | Q8C6L5 |
| D | DNA-F | dna | 15 | — | — |
| E | DNA-R | dna | 14 | — | — |
Ligands and binding sites
- GH3 · 3'-deoxy-guanosine-5'-triphosphate · ligand · chains A
- GDO · 3'-deoxy-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
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.75 | 0.95 | 18 | empty |
| 2 | 860 | 0.74 | 0.78 | 70 | MG, GH3, GDO |
| 3 | 537 | 0.60 | 0.74 | 31 | empty |
| 4 | 375 | 0.58 | 0.76 | 28 | empty |
| 5 | 175 | 0.54 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- D–E · 651 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–D · 512 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–E · 310 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4K99 · Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppdG(2 ,5 )pdG · 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 4K99 · PDBe 4K99 · UniProt Q8C6L5
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