Research workbench
Crystal structure of AGO2 mid domain in complex with 6-(3-(2- CARBOXYETHYL)PHENYL)PURINE riboside monophosphate
Analyse Crystal structure of AGO2 mid domain in complex with 6-(3-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C6B
- Type
- protein
- Length
- 400 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein argonaute-2
- EC
- 3.1.26.-
- UniProt
- Q9UKV8
- Ligands
- K2R, PO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein argonaute-2 (EC 3.1.26.-) | protein | 134 | 48% helix, 16% strand | Q9UKV8 |
| B | Protein argonaute-2 (EC 3.1.26.-) | protein | 132 | 48% helix, 17% strand | Q9UKV8 |
Ligands and binding sites
- K2R · 3-[3-[9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.67 | 0.74 | 83 | K2R |
| 2 | 79 | 0.33 | 0.75 | 14 | empty |
| 3 | 53 | 0.31 | 0.77 | 15 | K2R |
Interfaces
3 interfaces between chains.
- B–C · 696 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 179 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 162 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7C6B · Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKV8 · AlphaFold monomer V2.0 prediction for protein argonaute-2 (Q9UKV8) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 7C6B · PDBe 7C6B · UniProt Q9UKV8
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