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1l9k

dengue methyltransferase

Method: X-RAY DIFFRACTION Dmax: 71.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA-DIRECTED RNA POLYMERASE

Dengue virus

UniProt P12823

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 2492–2784 Fragment：NS5 N-terminal domain Mutation：V135I, K139R, N173S, P188S, R193K, T196A, Y201H SO4 SULFATE ION × 5 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；sodium citrate 100mM, lithium sulfate 1.2 M, ammonium sulfate 0.5 M, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 Å R-free 0.257
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2492–2784 Fragment：NS5 N-terminal domain Mutation：V135I, K139R, N173S, P188S, R193K, T196A, Y201H SO4 SULFATE ION × 10 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；sodium citrate 100mM, lithium sulfate 1.2 M, ammonium sulfate 0.5 M, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 Å R-free 0.257

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 1L9K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1OAN Crystal structure of the dengue 2 virus envelope protein Deposited 2003-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 281–674（394 aa） Fragment：SOLUBLE ECTODOMAIN, RESIDUES 281-674
Chain B 281–674（394 aa） Fragment：SOLUBLE ECTODOMAIN, RESIDUES 281-674
Not recorded NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；11% PEG 8000, 1 M NACL, 0.1 M TRIS/HCL PH 9.0, 20% GLYCEROL
Resolution 2.75 Å R-free 0.296
1OK8 Crystal structure of the dengue 2 virus envelope glycoprotein in the postfusion conformation Deposited 2003-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 281–674（394 aa） Fragment：SOLUBLE ECTODOMAIN, RESIDUES 281-674
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；20-30% PEG 400, 0.08 M NACL, 0.1 M MOPS PH 7-8.
Resolution 2.00 Å R-free 0.267
1OKE Crystal structure of the dengue 2 virus envelope protein in complex with n-octyl-beta-D-glucoside Deposited 2003-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 281–674（394 aa） Fragment：SOLUBLE ECTODOMAIN, RESIDUES 281-674
Chain B 281–674（394 aa） Fragment：SOLUBLE ECTODOMAIN, RESIDUES 281-674
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BOG octyl beta-D-glucopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；11% PEG 8K, 1M NACL, 0.1M TRIS/HCL PH 9.0, 20% GLYCEROL,0.5% OCTYLGLUCOSIDE
Resolution 2.40 Å R-free 0.294
1P58 Complex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction Deposited 2003-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 360 PDB declaration: 360-MERIC
Chain A 281–775（495 aa）
Chain B 281–775（495 aa）
Chain C 281–775（495 aa）
Chain D 206–280（75 aa）
Chain E 206–280（75 aa）
Chain F 206–280（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NaCl, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NaCl, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
1P58 Complex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction Deposited 2003-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 281–775（495 aa）
Chain B 281–775（495 aa）
Chain C 281–775（495 aa）
Chain D 206–280（75 aa）
Chain E 206–280（75 aa）
Chain F 206–280（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NaCl, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NaCl, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
1P58 Complex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction Deposited 2003-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 30 PDB declaration: 30-meric
Chain A 281–775（495 aa）
Chain B 281–775（495 aa）
Chain C 281–775（495 aa）
Chain D 206–280（75 aa）
Chain E 206–280（75 aa）
Chain F 206–280（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NaCl, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NaCl, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
1P58 Complex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction Deposited 2003-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 36 PDB declaration: 36-meric
Chain A 281–775（495 aa）
Chain B 281–775（495 aa）
Chain C 281–775（495 aa）
Chain D 206–280（75 aa）
Chain E 206–280（75 aa）
Chain F 206–280（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NaCl, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NaCl, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
1P58 Complex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction Deposited 2003-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 281–775（495 aa）
Chain B 281–775（495 aa）
Chain C 281–775（495 aa）
Chain D 206–280（75 aa）
Chain E 206–280（75 aa）
Chain F 206–280（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NaCl, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NaCl, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
1R6A Structure of the dengue virus 2'O methyltransferase in complex with s-adenosyl homocysteine and ribavirin 5' triphosphate Deposited 2003-10-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2492–2784（293 aa） Fragment：RNA-directed RNA polymerase (residue 2492-2784)
Not recorded SO4 SULFATE ION × 7 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 RVP RIBAVIRIN MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；Na Citrate 0.1 M, AS 0.5 M, LiSO4 1.2 M, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.243
1R6A Structure of the dengue virus 2'O methyltransferase in complex with s-adenosyl homocysteine and ribavirin 5' triphosphate Deposited 2003-10-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2492–2784（293 aa） Fragment：RNA-directed RNA polymerase (residue 2492-2784)
Not recorded SO4 SULFATE ION × 14 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 RVP RIBAVIRIN MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；Na Citrate 0.1 M, AS 0.5 M, LiSO4 1.2 M, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.243
1R6R Solution Structure of Dengue Virus Capsid Protein Reveals a New Fold Deposited 2003-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–100（100 aa） Fragment：capsid protein C (residue 1-100)
Chain B 1–100（100 aa） Fragment：capsid protein C (residue 1-100)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate and 200 mM NaCl；Pressure 1
NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate and 200 mM NaCl；Pressure 1
NMR sample composition 0.8 mM DEN2C protein U-15N, 13C; in 90% H2O/10% D2O with 50 mM sodium phosphate and 200 mM NaCl at pH 6.0. in SHIGEMI tube | 90% H2O/10% D2O
NMR sample composition 1mM or 2 mM DEN2C protein U-15N; in 90% H2O/10% D2O with 50 mM sodium phosphate and 200 mM NaCl at pH 6.0. in SHIGEMI tube | 90% H2O/10% D2O
Resolution not provided
1THD COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION Deposited 2004-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-MERIC
Chain A 281–675（395 aa）
Chain B 281–675（395 aa）
Chain C 281–675（395 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NACL, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NACL, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
1THD COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION Deposited 2004-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 281–675（395 aa）
Chain B 281–675（395 aa）
Chain C 281–675（395 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NACL, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NACL, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
1THD COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION Deposited 2004-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 281–675（395 aa）
Chain B 281–675（395 aa）
Chain C 281–675（395 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NACL, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NACL, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
1THD COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION Deposited 2004-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 281–675（395 aa）
Chain B 281–675（395 aa）
Chain C 281–675（395 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NACL, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NACL, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
1THD COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION Deposited 2004-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 281–675（395 aa）
Chain B 281–675（395 aa）
Chain C 281–675（395 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM TRIS, 75 mM NACL, 1 mM EDTA；pH 7.6；50 mM TRIS, 75 mM NACL, 1 mM EDTA
cryo-EM vitrification conditions SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Resolution 9.50 Å
3J8D Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5 Deposited 2014-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC
Chain G 281–674（394 aa） Fragment：UNP residues 281-674
Chain H 281–674（394 aa） Fragment：UNP residues 281-674
Chain I 281–674（394 aa） Fragment：UNP residues 281-674
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA；pH 5.5；120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane
Resolution 26.00 Å
3J8D Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5 Deposited 2014-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 281–674（394 aa） Fragment：UNP residues 281-674
Chain H 281–674（394 aa） Fragment：UNP residues 281-674
Chain I 281–674（394 aa） Fragment：UNP residues 281-674
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA；pH 5.5；120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane
Resolution 26.00 Å
3J8D Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5 Deposited 2014-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric
Chain G 281–674（394 aa） Fragment：UNP residues 281-674
Chain H 281–674（394 aa） Fragment：UNP residues 281-674
Chain I 281–674（394 aa） Fragment：UNP residues 281-674
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA；pH 5.5；120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane
Resolution 26.00 Å
3J8D Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5 Deposited 2014-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric
Chain G 281–674（394 aa） Fragment：UNP residues 281-674
Chain H 281–674（394 aa） Fragment：UNP residues 281-674
Chain I 281–674（394 aa） Fragment：UNP residues 281-674
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA；pH 5.5；120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane
Resolution 26.00 Å
3J8D Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5 Deposited 2014-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 281–674（394 aa） Fragment：UNP residues 281-674
Chain H 281–674（394 aa） Fragment：UNP residues 281-674
Chain I 281–674（394 aa） Fragment：UNP residues 281-674
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA；pH 5.5；120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane
Resolution 26.00 Å
5HHG Mouse importin alpha: Dengue 2 NS5 C-terminal NLS peptide complex Deposited 2016-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 3353–3388（36 aa） Fragment：UNP residues 3353-3388
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；1.5M Ammonium Sulfate, 0.1M Sodium HEPES
Resolution 2.20 Å R-free 0.214

9 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_DEN2P
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 13–305； UniProt 2492–2784

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 1l9k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1l9k
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1l9k
Deposition date deposition_date2002-03-25
Structure title titledengue methyltransferase
Keywords keywordsmethyltransferase fold, complex with s-adenosyl-l-homocysteine, 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_guinier19.22 Å
Radius of gyration Rg (electron density) rg_electron18.24 Å
Forward intensity I(0) i017404700.00
Molecular weight molecular_weight29950.0 kDa
Excluded volume excluded_volume36864 ų
Envelope volume envelope_volume42562 ų
Hydration-shell volume shell_volume19279 ų
Envelope diameter envelope_diameter66.4 Å
Shell Rg shell_rg24.76 Å
Envelope Rg envelope_rg18.61 Å
Shape Rg shape_rg18.25 Å
Total Rg total_rg19.11 Å
Total atoms total_atoms2093
Residues n_residues261
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 dmax71.8 Å
Rg (real space) rg_real19.11 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real1.7400e+07
I(0) uncertainty (real space) i0_real_error2.2540e+05
Rg (reciprocal space) rg_reciprocal19.12 Å
I(0) (reciprocal space) i0_reciprocal17400000.0000
Solution quality estimate total_estimate0.5803
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.207
Kurtosis Kurtosis kurtosis-0.312
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5434000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.569; Stabil: 1.000; Sysdev: 0.295; Positv: 1.000; Valcen: 0.948; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1l9ka_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.25 — mRNA cap methylase

CATH v4.4 (1 domains)

Domain ID domain_id1l9kA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
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8. Citations (1)

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9. Files and Curves (10)