3LUD

Crystal structure of MID domain from hAGO2 in complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 3LUD

Classification: RNA BINDING PROTEIN

Total Structure Weight: 47589.36

Macromolecule Entities
Molecule Chains Length Organism Details
Protein argonaute-2 A, B, C 138 Homo sapiens EC#: 3.1.26.n2 IUBMB
Fragment: MID domain
Gene Name(s): AGO2 Gene View EIF2C2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AMP
Query on AMP

A, B, C ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AMP N/A in BindingDB
Kd: 260000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.185
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 40.52 α = 86.36
b = 47.39 β = 72.71
c = 66.39 γ = 83.59

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-02-17
  • Released Date: 2010-05-26
  • Deposition author(s): Frank, F., Sonenberg, N., Nagar, B.

Revision History

  • 2011-07-13
    Type: Version format compliance