MolNFT v1 · #179856 · protein + RNA
Human ARGONAUTE2:MIR-122 bound to the HCV genotype 1A site-1 RNA
7KI3 · Protein argonaute-2: “Human ARGONAUTE2:MIR-122 bound to the HCV genotype 1A site-1 RNA”. X-ray diffraction, 1 ligand (BA), 20 pockets (best druggability 0.83). MolNFT v1 #179856 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7KI3
- Type
- protein + RNA
- Length
- 1,667 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein argonaute-2; Mir-122; HCV genotype 1A mir-122 site-1
- EC
- 3.1.26.-
- UniProt
- Q9UKV8
- Ligands
- BA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein argonaute-2 (EC 3.1.26.-) | protein | 804 | 31% helix, 25% strand | Q9UKV8 |
| B | Mir-122 | rna | 19 | — | — |
| C | HCV genotype 1A mir-122 site-1 | rna | 29 | — | — |
| D | Protein argonaute-2 (EC 3.1.26.-) | protein | 783 | 31% helix, 24% strand | Q9UKV8 |
| E | Mir-122 | rna | 11 | — | — |
| F | HCV genotype 1A mir-122 site-1 | rna | 21 | — | — |
Ligands and binding sites
- BA · Barium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.83 | 0.90 | 53 | empty |
| 2 | 1084 | 0.79 | 0.82 | 60 | BA |
| 3 | 1046 | 0.78 | 0.80 | 84 | empty |
| 4 | 154 | 0.72 | 0.91 | 25 | empty |
| 5 | 309 | 0.71 | 0.85 | 39 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2145 Ų buried · 46 hydrogen bonds · protein-nucleic
- D–E · 1525 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–C · 1306 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–F · 1088 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 1013 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 Q9UKV8
- Elsewhere: RCSB PDB 7KI3 · PDBe 7KI3 · UniProt Q9UKV8
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