Research workbench
The crystal structure of the ARGONAUTE2 paz domain (as a mbp fusion)
Analyse The crystal structure of the ARGONAUTE2 paz domain (as a mbp fusion) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R6Z
- Type
- protein
- Length
- 1,494 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of maltose-binding periplasmic protein and argonaute 2
- UniProt
- P02928
- Ligands
- GLC, NI
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Chimera of maltose-binding periplasmic protein and argonaute 2 | protein | 498 | 42% helix, 22% strand | P02928 |
| A | Chimera of maltose-binding periplasmic protein and argonaute 2 | protein | 497 | 41% helix, 22% strand | P02928 |
| Z | Chimera of maltose-binding periplasmic protein and argonaute 2 | protein | 499 | 41% helix, 22% strand | P02928 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains P, A, Z
- NI · Nickel (II) ion · metal · 9 copies · chains P, A, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.71 | 0.85 | 30 | GLC |
| 2 | 291 | 0.70 | 0.84 | 31 | GLC |
| 3 | 262 | 0.69 | 0.84 | 26 | GLC |
| 4 | 465 | 0.60 | 0.75 | 49 | empty |
| 5 | 509 | 0.60 | 0.74 | 53 | empty |
Interfaces
3 interfaces between chains.
- P–A · 215 Ų buried · 2 hydrogen bonds · protein-protein
- P–Z · 198 Ų buried · 1 hydrogen bond · protein-protein
- A–Z · 173 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1R6Z · The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion) · the same entry in another collection · chain P against P, 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 P02928
- Elsewhere: RCSB PDB 1R6Z · PDBe 1R6Z · UniProt P02928
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