9LMZ | pdb_00009lmz

hAGO2-MID in complex with a chemical modified uridine monophosphate

• PDB DOI: https://doi.org/10.2210/pdb9LMZ/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-01-20 Released: 2026-01-28 
• Deposition Author(s): Yao, Y.Q., Ma, J.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

hAGO2-MID in complex with a chemical modified uridine monophosphate

Yao, Y.Q., Ma, J.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.07 kDa 
• Atom Count: 3,573 
• Modeled Residue Count: 407 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-2	A, B, C	137	Homo sapiens	Mutation(s): 0  Gene Names: AGO2, EIF2C2 EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV8 (Homo sapiens) Explore Q9UKV8  Go to UniProtKB:  Q9UKV8
PHAROS:  Q9UKV8 GTEx:  ENSG00000123908

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EY1 (Subject of Investigation/LOI)	D [auth A], F [auth B], G [auth C]	[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)thieno[2,3-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate C11 H13 N2 O9 P S WTJWLDXEEZVLGX-JXOAFFINSA-N
ECC	E [auth B]	(4S)-4-amino-5-hydroxypentanamide C5 H12 N2 O2 FQLOSLKSJZSARD-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.561	α = 86.95
b = 46.536	β = 73.95
c = 66.277	γ = 85.04

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Yao, Y.Q., Ma, J.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971130

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release