6C8M

RNA-activated 2-AIpG monomer, 1.5h soaking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystallographic observation of nonenzymatic RNA primer extension

Zhang, W.Walton, T.Li, L.Szostak, J.W.

(2018) Elife 7: e36422


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3')A15synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')B14synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EQ1
Query on EQ1

Download SDF File 
Download CCD File 
A
[2-azanyl-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-1-yl]-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]phosphinic acid
C23 H30 N13 O14 P2
VUFFAXSZAZXUSC-XPWFQUROSA-N
 Ligand Interaction
EQ4
Query on EQ4

Download SDF File 
Download CCD File 
A
5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine
C13 H17 N8 O7 P
UJFHHYLHXPKINK-IOSLPCCCSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LCG
Query on LCG
A, B
RNA LINKINGC11 H14 N5 O8 PDG
LCC
Query on LCC
A, B
RNA LINKINGC11 H16 N3 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.240 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 47.874α = 90.00
b = 47.874β = 90.00
c = 82.731γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release