2XZL

Upf1-RNA complex

Structural Biology Knowledgebase: 2XZL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2XZL

Classification: HYDROLASE / RNA

Total Structure Weight: 96318.41


Macromolecule Entities
Molecule Chains Length Organism Details
ATP-DEPENDENT HELICASE NAM7 A 802 Saccharomyces cerevisiae EC#: 3.4.23.50 IUBMB
Fragment: CH DOMAIN AND HELICASE DOMAIN, RESIDUES 54-850
Gene Name(s): NAM7 IFS2 MOF4 UPF1 Gene View YMR080C YM9582.05C
Macromolecule Entities
Molecule Chains Length Organism Details
5- R(*UP*UP*UP*UP*UP*UP*UP*UP*U) -3 B 9 Synthetic construct

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1PE
Query on 1PE

A PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ALF
Query on ALF

A TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.197
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 64.14 α = 90.00
b = 114.12 β = 110.24
c = 65.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-11-26
  • Released Date: 2011-03-30
  • Deposition author(s): Chakrabarti, S., Jayachandran, U., Bonneau, F., Fiorini, F., Basquin, C., Domcke, S., Le Hir, H., Conti, E.

Revision History

No revisions since initial release