MolNFT v1 · #145009 · protein + RNA

Crystal structure of human ARGONAUTE2 bound to three tryptophans

6CBD · Protein argonaute-2: “Crystal structure of human ARGONAUTE2 bound to three tryptophans”. X-ray diffraction, 2 ligands (TRP, MG), 8 pockets (best druggability 0.88). MolNFT v1 #145009 on GenesisL1: 3D structure, binding sites and…

PDB: 6CBD
Type: protein + RNA
Length: 814 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein argonaute-2; Guide RNA; Target RNA
EC: 3.1.26.-
UniProt: Q9UKV8
Ligands: TRP, MG
Pockets: 8 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein argonaute-2 (EC 3.1.26.-)	protein	787	31% helix, 27% strand	Q9UKV8
B	Guide RNA	rna	18	—	—
C	Target RNA	rna	9	—	—

Ligands and binding sites

TRP · Tryptophan · ligand · 3 copies · chains A
MG · Magnesium ion · metal · 3 copies · chains A, B, C
IPA · Isopropyl alcohol · additive · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1131	0.88	0.89	109	MG
2	137	0.67	0.89	19	empty
3	271	0.63	0.81	32	empty
4	53	0.50	0.87	14	IPA
5	109	0.45	0.79	25	empty

Interfaces

3 interfaces between chains.

A–B · 2338 Å² buried · 64 hydrogen bonds · protein-nucleic
A–C · 935 Å² buried · 14 hydrogen bonds · protein-nucleic
B–C · 402 Å² buried · 33 hydrogen bonds · nucleic-nucleic

Compared structures

6CBD · Crystal Structure of Human Argonaute2 Bound to Three Tryptophans · 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 A against A, TM-score 0.98

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 6CBD · PDBe 6CBD · UniProt Q9UKV8

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