Research workbench
Two mouse cgas catalytic domain binding to human assembled nucleosome
Analyse Two mouse cgas catalytic domain binding to human assembled nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XJD
- Type
- protein + DNA
- Length
- 1,775 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B type 1-C/E/F/G/I; DNA…
- EC
- 2.7.7.86
- UniProt
- Q71DI3, P62805, P0C0S8, P62807, Q8C6L5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 98 | 65% helix, 1% strand | Q71DI3 |
| B | Histone H4 | protein | 80 | 56% helix, 3% strand | P62805 |
| C | Histone H2A type 1 | protein | 108 | 49% helix, 4% strand | P0C0S8 |
| D | Histone H2B type 1-C/E/F/G/I | protein | 95 | 72% helix, 2% strand | P62807 |
| F | Histone H4 | protein | 81 | 59% helix, 4% strand | P62805 |
| G | Histone H2A type 1 | protein | 107 | 53% helix, 1% strand | P0C0S8 |
| H | Histone H2B type 1-C/E/F/G/I | protein | 94 | 71% helix, 0% strand | P62807 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| K, L | Cyclic gmp-AMP synthase (EC 2.7.7.86) | protein | 362 | 40% helix, 16% strand | Q8C6L5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.85 | 0.85 | 90 | empty |
| 2 | 1088 | 0.85 | 0.85 | 92 | empty |
| 3 | 705 | 0.79 | 0.83 | 93 | empty |
| 4 | 180 | 0.79 | 0.94 | 42 | empty |
| 5 | 566 | 0.78 | 0.84 | 54 | empty |
Interfaces
38 interfaces between chains.
- I–J · 6622 Ų buried · 766 hydrogen bonds · nucleic-nucleic
- E–F · 2413 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2358 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2325 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2290 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6XJD · Two mouse cGAS catalytic domain binding to human assembled nucleosome · the same entry in another collection · chain L against L, 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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P0C0S8
- Every structure of UniProt P62807
- Every structure of UniProt Q8C6L5
- Elsewhere: RCSB PDB 6XJD · PDBe 6XJD · UniProt Q71DI3 · UniProt P62805 · UniProt P0C0S8 · UniProt P62807 · UniProt Q8C6L5
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