5MRK

Structural basis of Zika virus methyltransferase inhibition by sinefungin

PDB DOI: https://doi.org/10.2210/pdb5MRK/pdb

Classification: TRANSFERASE
Organism(s): Zika virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-23 Released: 2017-01-25
Deposition Author(s): Hercik, K., Boura, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.269
R-Value Work: 0.227
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural basis of Zika virus methyltransferase inhibition by sinefungin.

Hercik, K., Brynda, J., Nencka, R., Boura, E.

(2017) Arch Virol 162: 2091-2096

PubMed: 28357511 Search on PubMed
DOI: https://doi.org/10.1007/s00705-017-3345-x
Primary Citation of Related Structures:
5MRK

PubMed Abstract:
Zika virus is considered a major global threat to human kind. Here, we present a crystal structure of one of its essential enzymes, the methyltransferase, with the inhibitor sinefungin. This structure, together with previously solved structures with bound substrates, will provide the information needed for rational inhibitor design. Based on the structural data we suggest the modification of the adenine moiety of sinefungin to increase selectivity and to covalently link it to a GTP analogue, to increase the affinity of the synthesized compounds.

Organizational Affiliation

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic.

Macromolecule Content

Total Structure Weight: 59.46 kDa
Atom Count: 4,316
Modelled Residue Count: 505
Deposited Residue Count: 530
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methyltransferase	A, B	265	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1 Go to UniProtKB: A0A024B7W1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A024B7W1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFG Query on SFG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.269
R-Value Work: 0.227
R-Value Observed: 0.229
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.84	α = 90
b = 52.01	β = 107.56
c = 84.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Hercik, K.

Boura, E.

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2017-05-17
Changes: Database references
Version 1.2: 2017-06-28
Changes: Database references
Version 1.3: 2024-01-17
Changes: Advisory, Data collection, Database references, Refinement description