5IKM

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, Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.184
R-Value Work: 0.153
R-Value Observed: 0.154

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6XG39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
BDF Query on BDF Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	beta-D-fructopyranose C₆ H₁₂ O₆ LKDRXBCSQODPBY-ARQDHWQXSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] 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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on 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
R-Value Work: 0.153
R-Value Observed: 0.154
Space Group: I 2 2 2
Diffraction Data: https://doi.org/10.18430/m35ikm

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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