MolNFT v1 · #146139 · protein + DNA + RNA
Ternary rsago complex containing guide RNA paired with target DNA
6D8P · Uncharacterized protein: “Ternary rsago complex containing guide RNA paired with target DNA”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.85). MolNFT v1 #146139 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6D8P
- Type
- protein + DNA + RNA
- Length
- 1,585 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 0.85
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, 29% strand | A4WYU7 |
| E, C | 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 | — | — |
| J | DNA (5'- D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*AP*C)-3') | dna | 19 | — | — |
| B | Uncharacterized protein | protein | 752 | 32% helix, 28% strand | A4WYU7 |
| G | DNA (5'- D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*AP*C)-3') | dna | 20 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, E, B, C
- ACT · Acetate ion · additive · 20 copies · chains A, J, E, B, C, G
- CAC · Cacodylate ion · additive · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.85 | 0.86 | 81 | ACT |
| 2 | 899 | 0.84 | 0.86 | 75 | ACT |
| 3 | 224 | 0.80 | 0.94 | 28 | empty |
| 4 | 145 | 0.77 | 0.94 | 23 | empty |
| 5 | 128 | 0.77 | 0.95 | 24 | ACT |
Interfaces
7 interfaces between chains.
- A–J · 1863 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–E · 1844 Ų buried · 52 hydrogen bonds · protein-nucleic
- B–C · 1790 Ų buried · 52 hydrogen bonds · protein-nucleic
- B–G · 1731 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–G · 807 Ų buried · 77 hydrogen bonds · nucleic-nucleic
Compared structures
- 6D8P · Ternary RsAgo Complex Containing Guide RNA Paired with Target DNA · 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 6D8P · PDBe 6D8P · UniProt A4WYU7
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