Research workbench
Ternary rsago complex with guide RNA and target DNA containing a-G non-canonical pair
Analyse Ternary rsago complex with guide RNA and target DNA containing a-G… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D9K
- Type
- protein + DNA + RNA
- Length
- 1,589 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; RNA (5'- R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A…
- UniProt
- A4WYU7
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 758 | 32% helix, 28% strand | A4WYU7 |
| C, H | RNA (5'- R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3') | rna | 18 | — | — |
| G | DNA (5'- D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*GP*GP*CP*AP*GP*TP*AP*AP*C)-3') | dna | 19 | — | — |
| F | Uncharacterized protein | protein | 755 | 32% helix, 29% strand | A4WYU7 |
| J | DNA (5'- D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*GP*GP*CP*AP*GP*TP*AP*AP*C)-3') | dna | 21 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, F, H
- ACT · Acetate ion · additive · 3 copies · chains A, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, F, H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.84 | 0.86 | 81 | empty |
| 2 | 918 | 0.84 | 0.86 | 77 | empty |
| 3 | 181 | 0.79 | 0.94 | 26 | empty |
| 4 | 162 | 0.78 | 0.95 | 23 | empty |
| 5 | 870 | 0.76 | 0.79 | 42 | empty |
Interfaces
8 interfaces between chains.
- A–G · 1875 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 1850 Ų buried · 53 hydrogen bonds · protein-nucleic
- F–J · 1848 Ų buried · 19 hydrogen bonds · protein-nucleic
- F–H · 1800 Ų buried · 47 hydrogen bonds · protein-nucleic
- H–J · 828 Ų buried · 69 hydrogen bonds · nucleic-nucleic
Compared structures
- 6D9K · Ternary RsAgo Complex with Guide RNA and Target DNA Containing A-G Non-canonical Pair · 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 A4WYU7
- Elsewhere: RCSB PDB 6D9K · PDBe 6D9K · UniProt A4WYU7
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