Research workbench
X-ray crystal structure of marinitoga piezophila argonaute in complex with 5' oh guide RNA and target DNA
Analyse X-ray crystal structure of marinitoga piezophila argonaute in complex with 5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UX0
- Type
- protein + DNA + RNA
- Length
- 1,345 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute protein; RNA (5'- R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)…
- UniProt
- H2J4R4
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute protein | protein | 632 | 30% helix, 30% strand | H2J4R4 |
| B | RNA (5'- R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3') | rna | 20 | — | — |
| C | DNA (5'- D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3') | dna | 20 | — | — |
| D | Argonaute protein | protein | 639 | 31% helix, 30% strand | H2J4R4 |
| E | RNA (5'- R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3') | rna | 18 | — | — |
| F | DNA (5'- D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3') | dna | 16 | — | — |
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.88 | 0.90 | 126 | empty |
| 2 | 891 | 0.85 | 0.87 | 71 | empty |
| 3 | 89 | 0.75 | 0.97 | 20 | empty |
| 4 | 287 | 0.69 | 0.84 | 31 | empty |
| 5 | 348 | 0.66 | 0.80 | 39 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1614 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–B · 1580 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–C · 1120 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–F · 1042 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 851 Ų buried · 61 hydrogen bonds · nucleic-nucleic
Compared structures
- 5UX0 · X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide… · 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 H2J4R4
- Elsewhere: RCSB PDB 5UX0 · PDBe 5UX0 · UniProt H2J4R4
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