Research workbench
Crystal structure of AGO2 mid domain in complex with 8-br-adenosin-5'- monophosphate
Analyse Crystal structure of AGO2 mid domain in complex with 8-br-adenosin-5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D7U
- Type
- protein
- Length
- 401 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
- 8BR
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein argonaute-2 (EC 3.1.26.-) | protein | 133 | 46% helix, 17% strand | Q9UKV8 |
| C | Protein argonaute-2 (EC 3.1.26.-) | protein | 135 | 45% helix, 16% strand | Q9UKV8 |
Ligands and binding sites
- 8BR · 8-bromo-adenosine-5'-monophosphate · ligand · 3 copies · chains A, B, 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 | 366 | 0.59 | 0.76 | 42 | empty |
| 2 | 122 | 0.42 | 0.76 | 30 | 8BR |
| 3 | 50 | 0.29 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 411 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 283 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 61 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7D7U · Crystal structure of Ago2 MID domain in complex with 8-Br-adenosin-5'-monophosphate · 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 7D7U · PDBe 7D7U · UniProt Q9UKV8
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