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Crystal structure of aa-ago with externally-bound siRNA

Analyse Crystal structure of aa-ago with externally-bound siRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F8T
Type: protein + RNA
Length: 1,458 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 26-mer; Argonaute protein
UniProt: O67434
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	26-mer	rna	26	—	—
D	26-mer	rna	24	—	—
A, B	Argonaute protein	protein	704	33% helix, 30% strand	O67434

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1198	0.75	0.78	93	empty
2	480	0.74	0.83	48	empty
3	352	0.67	0.81	41	empty
4	397	0.65	0.79	68	empty
5	283	0.64	0.81	36	empty

Interfaces

4 interfaces between chains.

C–D · 1165 Å² buried · 129 hydrogen bonds · nucleic-nucleic
A–B · 1088 Å² buried · 14 hydrogen bonds · protein-protein
C–A · 498 Å² buried · 7 hydrogen bonds · protein-nucleic
D–A · 76 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

2F8T · Crystal structure of Aa-Ago with externally-bound siRNA · the same entry in another collection · chain C against C, 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 O67434
Elsewhere: RCSB PDB 2F8T · PDBe 2F8T · UniProt O67434

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