8ZMC | pdb_00008zmc

Dengue 3 NS5 methyltransferase bound to S-Adenosyl-L-homocysteine and Herbacetin

PDB DOI: https://doi.org/10.2210/pdb8ZMC/pdb

Classification: TRANSFERASE
Organism(s): dengue virus type 3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-23 Released: 2025-05-28
Deposition Author(s): Bhutkar, M., Verma, S., Tomar, S., Kumar, P.
Funding Organization(s): Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.302 (Depositor), 0.295 (DCC)
R-Value Work:
0.259 (Depositor), 0.259 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Dengue 3 NS5 methyltransferase bound to S-Adenosyl-L-homocysteine and Herbacetin

Bhutkar, M., Verma, S., Tomar, S., Kumar, P.

To be published.

Macromolecule Content

Total Structure Weight: 65.63 kDa
Atom Count: 4,180
Modeled Residue Count: 512
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dengue 3 NS5 methyltransferase	A, B	284	dengue virus type 3	Mutation(s): 0 EC: 2.1.1.358
UniProt
Find proteins for C1KBQ3 (dengue virus type 3) Explore C1KBQ3 Go to UniProtKB: C1KBQ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1KBQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
A1L1Z (Subject of Investigation/LOI) Query on A1L1Z Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	Herbacetin C₁₅ H₁₀ O₇ ZDOTZEDNGNPOEW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File 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 J [auth B] 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 J [auth B] 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 J [auth B]	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B]