5VAJ

BhRNase H - amide-RNA/DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.166

Literature

Macromolecules
Sequence Display for 5VAJ

Classification: hydrolase / rna / dna

Total Structure Weight: 41197.95


Macromolecule Entities
Molecule Chains Length Organism Details
Ribonuclease H A, B 142 Bacillus halodurans EC#: 3.1.26.4 IUBMB
Mutation: D132N
Gene Name(s): rnhA BH0863
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*(URU)P*C)-3') C 11 Synthetic construct
DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3') D 12 Synthetic construct

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

A, B, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
URU
Query on URU
C RNA LINKING C20 H26 N5 O14 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.166
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 137.18 α = 90.00
b = 37.51 β = 121.65
c = 93.86 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-03-27
  • Released Date: 2017-09-13
  • Deposition author(s): Pallan, P.S., Egli, M.

Revision History

No revisions since initial release