MolNFT v1 · #121739 · protein + RNA
X-ray crystal structure of marinitoga piezophila argonaute in complex with 5' oh guide RNA
5I4A · Argonaute protein: “X-ray crystal structure of marinitoga piezophila argonaute in complex with 5' oh guide RNA”. X-ray diffraction, 14 pockets (best druggability 0.78). MolNFT v1 #121739 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5I4A
- Type
- protein + RNA
- Length
- 1,290 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute protein; RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*U)-3')
- UniProt
- H2J4R4
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute protein | protein | 631 | 30% helix, 32% strand | H2J4R4 |
| B, D | RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*U)-3') | rna | 12 | — | — |
| C | Argonaute protein | protein | 635 | 31% helix, 33% strand | H2J4R4 |
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 | 1106 | 0.78 | 0.80 | 85 | empty |
| 2 | 1048 | 0.77 | 0.79 | 67 | empty |
| 3 | 529 | 0.67 | 0.78 | 41 | empty |
| 4 | 539 | 0.66 | 0.77 | 50 | empty |
| 5 | 524 | 0.65 | 0.77 | 66 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1703 Ų buried · 32 hydrogen bonds · protein-nucleic
- C–D · 1629 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–C · 267 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5I4A · X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA · 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 5I4A · PDBe 5I4A · UniProt H2J4R4
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