4KZD

Crystal structure of an RNA aptamer in complex with fluorophore and Fab

Structural Biology Knowledgebase: 4KZD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KZD

Classification: immune system / rna

Total Structure Weight: 76087.10


Macromolecule Entities
Molecule Chains Length Organism Details
BL3-6 Fab antibody, heavy chain H 232 Mus musculus
BL3-6 Fab antibody, light chain L 215 Mus musculus
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (84-MER) R 84 synthetic Spinach RNA aptamer

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SUC
Query on SUC

H SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1TU
Query on 1TU

R 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl- 1H-imidazol-5-ol
C12 H12 F2 N2 O2
MSZRPLCUVKFQJC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

R POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

R MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
GDP
Query on GDP
R RNA LINKING C10 H15 N5 O11 P2 G

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.179
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 148.43 α = 90.00
b = 79.60 β = 111.65
c = 95.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-29
  • Released Date: 2014-06-18
  • Deposition author(s): Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

Revision History

  • 2015-05-20
    Type: Polymer description | Details: --
  • 2014-07-30
    Type: Citation | Details: Citation update
  • 2014-07-09
    Type: Citation | Details: Citation update