2HVY

Crystal structure of an H/ACA box RNP from Pyrococcus furiosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.238

Literature

Macromolecules
Sequence Display for 2HVY

Classification: ISOMERASE / BIOSYNTHETIC PROTEIN / RNA

Total Structure Weight: 94918.87


Macromolecule Entities
Molecule Chains Length Organism Details
Probable tRNA pseudouridine synthase B A 346 Pyrococcus furiosus EC#: 5.4.99.25 IUBMB
Gene Name(s): truB PF1785
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small nucleolar rnp similar to gar1 B 104 Pyrococcus furiosus Gene Name(s): PF1791
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ribosome biogenesis protein Nop10 C 60 Pyrococcus furiosus Mutation: R2K
Gene Name(s): nop10 PF1141
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L7Ae D 130 Pyrococcus furiosus Mutation: M2A
Gene Name(s): rpl7ae PF1367
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
H/ACA RNA E 65 synthetic

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

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.238
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 83.03 α = 90.00
b = 90.95 β = 90.00
c = 114.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-07-31
  • Released Date: 2006-09-12
  • Deposition author(s): Ye, K.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4