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9x7t

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

Method: X-RAY DIFFRACTION Dmax: 89.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NS5 methyltransferase

dengue virus type 3

UniProt C1KBQ3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2491–2755 Not recorded Herbacetin × 1 S-ADENOSYL-L-HOMOCYSTEINE × 1 GLYCEROL × 5 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å R-free 0.299
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 2491–2755 Not recorded S-ADENOSYL-L-HOMOCYSTEINE × 1 GLYCEROL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å R-free 0.299

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9X7T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3P8Z Dengue Methyltransferase bound to a SAM-based inhibitor Deposited 2010-10-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2491–2752（262 aa） Fragment：Methyltransferase
Not recorded 36A (S)-2-amino-4-(((2S,3S,4R,5R)-5-(6-(3-chlorobenzylamino)-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methylthio)butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；pH 8.5, VAPOR DIFFUSION, temperature 291K
Resolution 1.70 Å R-free 0.231
3P8Z Dengue Methyltransferase bound to a SAM-based inhibitor Deposited 2010-10-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2491–2752（262 aa） Fragment：Methyltransferase
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；pH 8.5, VAPOR DIFFUSION, temperature 291K
Resolution 1.70 Å R-free 0.231
3P97 Dengue 3 NS5 Methyltransferase bound to the substrate S-Adenosyl methionine Deposited 2010-10-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2491–2752（262 aa） Fragment：N-terminal domain
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；22.5% Peg8000, 200mM NaCl, 20mM Na3Citrate, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 291K
Resolution 1.70 Å R-free 0.221
3P97 Dengue 3 NS5 Methyltransferase bound to the substrate S-Adenosyl methionine Deposited 2010-10-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2491–2752（262 aa） Fragment：N-terminal domain
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；22.5% Peg8000, 200mM NaCl, 20mM Na3Citrate, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 291K
Resolution 1.70 Å R-free 0.221
4R05 Crystal structure of the refolded DENV3 methyltransferase Deposited 2014-07-29 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2491–2752（262 aa） Fragment：UNP residues 2491-2752
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；50 mM sodium citrate, pH 5.6, 24-30% PEG 4,000, 5% saturated ammonium sulfate, 10% glycerol, 0-20% DMSO, and 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.307
4R05 Crystal structure of the refolded DENV3 methyltransferase Deposited 2014-07-29 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2491–2752（262 aa） Fragment：UNP residues 2491-2752
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；50 mM sodium citrate, pH 5.6, 24-30% PEG 4,000, 5% saturated ammonium sulfate, 10% glycerol, 0-20% DMSO, and 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.307
4R8R Dengue virus serotype 3 methyltransferase without a bound S-adenosyl methionine Deposited 2014-09-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2491–2752（262 aa） Fragment：N-terminal domain, UNP residues 2491-2752
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；22.5% PEG 8000, 0.2M NaCl, 0.1M Tris-HCl, 20mM tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.46 Å R-free 0.218
4R8R Dengue virus serotype 3 methyltransferase without a bound S-adenosyl methionine Deposited 2014-09-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2491–2752（262 aa） Fragment：N-terminal domain, UNP residues 2491-2752
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；22.5% PEG 8000, 0.2M NaCl, 0.1M Tris-HCl, 20mM tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.46 Å R-free 0.218
4R8S Dengue serotype 3 methyltransferase bound to Sinefungin Deposited 2014-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2491–2752（262 aa） Fragment：N-terminal domain, UNP residues 2491-2752
Not recorded SFG SINEFUNGIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；22.5% PEG 8000, 0.2M NaCl, 0.1M Tris-HCl, 20mM tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.48 Å R-free 0.214
4R8S Dengue serotype 3 methyltransferase bound to Sinefungin Deposited 2014-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2491–2752（262 aa） Fragment：N-terminal domain, UNP residues 2491-2752
Not recorded SFG SINEFUNGIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；22.5% PEG 8000, 0.2M NaCl, 0.1M Tris-HCl, 20mM tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.48 Å R-free 0.214
8KDZ DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-Adenosyl-L-homocysteine and Caffeic acid phenethyl ester Deposited 2023-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2491–2755（265 aa）
Chain B 2491–2755（265 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 QAP 2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25% PEG 8000 100 mM Tris 200 mM NaCl 20 mM Trisodium citrate
Resolution 2.60 Å R-free 0.273

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C1KBQ3_9FLAV
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 20–284； UniProt 2491–2755 Author chain B； PDBConstruct 20–284； UniProt 2491–2755

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9x7t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9x7t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9x7t
Deposition date deposition_date2025-10-17
最后修订 last_revision2026-06-10
Structure title titleDengue 3 NS5 methyltransferase bound to S-Adenosyl-L-homocysteine and Herbacetin
Keywords keywordsDengue 3, NS5 methyltransferase, S-Adenosyl-L-homocysteine, Herbacetin, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.59 Å
Radius of gyration Rg (electron density) rg_electron26.93 Å
Forward intensity I(0) i0115021000.00
Molecular weight molecular_weight55479.0 kDa
Excluded volume excluded_volume53058 ų
Envelope volume envelope_volume91354 ų
Hydration-shell volume shell_volume28586 ų
Envelope diameter envelope_diameter94.6 Å
Shell Rg shell_rg33.86 Å
Envelope Rg envelope_rg27.15 Å
Shape Rg shape_rg26.93 Å
Total Rg total_rg27.46 Å
Total atoms total_atoms4186
Residues n_residues512
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.7 Å
Rg (real space) rg_real27.64 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real1.1500e+08
I(0) uncertainty (real space) i0_real_error1.6600e+06
Rg (reciprocal space) rg_reciprocal27.63 Å
I(0) (reciprocal space) i0_reciprocal115000000.0000
Solution quality estimate total_estimate0.8946
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3 Å
Skewness Skewness skewness0.341
Kurtosis Kurtosis kurtosis-0.558
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13910000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.979
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)