3EVC

Crystal structure of GTP complex of yellow fever virus methyltransferase and S-adenosyl-L-homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 3EVC

Classification: TRANSFERASE

Total Structure Weight: 32198.40

Macromolecule Entities
Molecule Chains Length Organism Details
RNA-directed RNA polymerase NS5 A 277 Yellow fever virus EC#: 2.1.1.56 IUBMB 2.7.7.48 IUBMB
Fragment: N-terminal domain 1-268 of RNA-directed RNA polymerase NS5: UNP residues 2507-2772
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SAH
Query on SAH

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GTP N/A in BindingDB
N/A in BindingMoad
Kd: 124 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.203
  • Space Group: P 65

Unit Cell:

Length (Å) Angle (°)
a = 104.47 α = 90.00
b = 104.47 β = 90.00
c = 51.71 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-10-13
  • Released Date: 2009-01-06
  • Deposition author(s): Thompson, A.A., Geiss, B.J., Peersen, O.B.

Revision History

  • Version 1_0: 2009-01-06

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Source and taxonomy, Version format compliance