2P1D

Crystal structure of dengue methyltransferase in complex with GTP and S-Adenosyl-L-homocysteine

Structural Biology Knowledgebase: 2P1D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Observed: 0.211

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2P1D

Classification: VIRAL PROTEIN TRANSFERASE

Total Structure Weight: 36105.51

Macromolecule Entities
Molecule Chains Length Organism Details
type II methyltransferase A 305 Dengue virus EC#: 2.7.7.48 IUBMB
Fragment: residues 1-296
Mutation: M70L, K139R, N173S, I180V, P188S, Y201H, I271T
Gene Name(s):

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

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
5GP
Query on 5GP

A GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Observed: 0.211
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 112.20 α = 90.00
b = 112.20 β = 90.00
c = 56.46 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-05
  • Released Date: 2007-03-20
  • Deposition author(s): Egloff, M.P., Benarooch, D., Marseilles Structural Genomics Program @ AFMB (MSGP)

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4