5UC6

Structural insights into IL-1 alpha recognition by a naphthyl-modified aptamer that mimics IL-1RI Domain III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 5UC6

Classification: IMMUNE SYSTEM / DNA

Total Structure Weight: 26646.56


Macromolecule Entities
Molecule Chains Length Organism Details
Interleukin-1 alpha A 159 Homo sapiens Fragment: residues 113-271
Gene Name(s): IL1A Gene View IL1F1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*G)-R(P*(85Y))-D(P*GP*AP*G)-R(P*(85Y)P*(85Y))-D(P*A)-R(P*(85Y))-D(P*GP*GP*G)-R(P*(85Y)P*(85Y))-D(P*AP*GP*AP*G)-R(P*(85Y))-D(P*CP*GP*(ATD))-3') B 23 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
85Y
Query on 85Y
B RNA linking C21 H22 N3 O9 P U
ATD
Query on ATD
B DNA LINKING C10 H15 N2 O8 P DT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.178
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 74.79 α = 90.00
b = 74.79 β = 90.00
c = 86.36 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-12-21
  • Released Date: 2017-10-11
  • Deposition author(s): Ren, X., Pyle, A.

Revision History

  • Version 1_0: 2017-10-11

    Type: Initial release

  • Version 1_1: 2017-10-18

    Type: Database references

  • Version 2_0: 2017-11-15

    Type: Atomic model, Derived calculations, Non-polymer description, Structure summary