MolNFT v1 · #113920 · protein + DNA + RNA
Rhodobacter sphaeroides argonaute in complex with guide RNA/TARGET DNA heteroduplex
5AWH · Uncharacterized protein: “Rhodobacter sphaeroides argonaute in complex with guide RNA/TARGET DNA heteroduplex”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.85). MolNFT v1 #113920 on GenesisL1: 3D structure…
- PDB
- 5AWH
- Type
- protein + DNA + RNA
- Length
- 1,546 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; RNA (5'- D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G…
- UniProt
- A4WYU7
- Ligands
- MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 759 | 33% helix, 28% strand | A4WYU7 |
| B | Uncharacterized protein | protein | 715 | 32% helix, 27% strand | A4WYU7 |
| C, E | RNA (5'- D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3') | rna | 18 | — | — |
| D, F | DNA (5'- D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3') | dna | 18 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.85 | 0.86 | 82 | empty |
| 2 | 209 | 0.81 | 0.95 | 28 | empty |
| 3 | 199 | 0.80 | 0.95 | 28 | empty |
| 4 | 576 | 0.79 | 0.86 | 44 | empty |
| 5 | 379 | 0.77 | 0.87 | 38 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1882 Ų buried · 62 hydrogen bonds · protein-nucleic
- A–C · 1830 Ų buried · 57 hydrogen bonds · protein-nucleic
- B–F · 1778 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 1755 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–D · 800 Ų buried · 63 hydrogen bonds · nucleic-nucleic
Compared structures
- 5AWH · Rhodobacter sphaeroides Argonaute in complex with guide RNA/target DNA heteroduplex · 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 5AWH · PDBe 5AWH · UniProt A4WYU7
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