5IKM | pdb_00005ikm

1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.

• PDB DOI: https://doi.org/10.2210/pdb5IKM/pdb

• Classification: TRANSFERASE
• Organism(s): dengue virus type 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-03 Released: 2016-03-16 
• Deposition Author(s): Minasov, G., Shuvalova, L., Winsor, J., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.153 (Depositor) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.

Minasov, G., Shuvalova, L., Winsor, J., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.91 kDa 
• Atom Count: 2,610 
• Modeled Residue Count: 259 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NS5 Methyl Transferase	A	269	dengue virus type 1	Mutation(s): 0
UniProt
Find proteins for I6XG39 (Dengue virus type 1) Explore I6XG39  Go to UniProtKB:  I6XG39

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	L [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
BDF	M [auth A]	beta-D-fructopyranose C6 H12 O6 LKDRXBCSQODPBY-ARQDHWQXSA-N
MLT	N [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	O [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.153 (Depositor) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35ikm

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.38	α = 90
b = 86.23	β = 90
c = 144.307	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Minasov, G., Shuvalova, L., Winsor, J., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary
• Version 1.6: 2025-10-22
  Changes: Database references, Structure summary