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3vdd

Structure of HRV2 capsid complexed with antiviral compound BTA798

Method: X-RAY DIFFRACTION Dmax: 93.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein VP1

OrganismNot specified

UniProt P04936

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 homooligomer Homooligomer Protein × 240 PDB declaration: 240-MERIC（240） Consistent with protein copy count Chain A； UniProt 568–850 Chain B； UniProt 70–330 Chain C； UniProt 331–567 Chain D； UniProt 1–69 Fragment：UNP residues 568-850 Fragment：UNP residues 70-330 Fragment：UNP residues 331-567 Fragment：UNP residues 1-69 BT8 3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole × 60 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；298 K；0.4-0.7 M ammonium sulfate, pH 7.5, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.273
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 568–850 Chain B； UniProt 70–330 Chain C； UniProt 331–567 Chain D； UniProt 1–69 Fragment：UNP residues 568-850 Fragment：UNP residues 70-330 Fragment：UNP residues 331-567 Fragment：UNP residues 1-69 BT8 3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；298 K；0.4-0.7 M ammonium sulfate, pH 7.5, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.273
3 Protein homooligomer Homooligomer Protein × 20 PDB declaration: eicosameric（20） Consistent with protein copy count Chain A； UniProt 568–850 Chain B； UniProt 70–330 Chain C； UniProt 331–567 Chain D； UniProt 1–69 Fragment：UNP residues 568-850 Fragment：UNP residues 70-330 Fragment：UNP residues 331-567 Fragment：UNP residues 1-69 BT8 3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole × 5 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；298 K；0.4-0.7 M ammonium sulfate, pH 7.5, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.273
4 Protein homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count Chain A； UniProt 568–850 Chain B； UniProt 70–330 Chain C； UniProt 331–567 Chain D； UniProt 1–69 Fragment：UNP residues 568-850 Fragment：UNP residues 70-330 Fragment：UNP residues 331-567 Fragment：UNP residues 1-69 BT8 3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole × 6 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；298 K；0.4-0.7 M ammonium sulfate, pH 7.5, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.273
5 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 568–850 Chain B； UniProt 70–330 Chain C； UniProt 331–567 Chain D； UniProt 1–69 Fragment：UNP residues 568-850 Fragment：UNP residues 70-330 Fragment：UNP residues 331-567 Fragment：UNP residues 1-69 BT8 3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；298 K；0.4-0.7 M ammonium sulfate, pH 7.5, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.273
6 Protein homooligomer Homooligomer Protein × 120 PDB declaration: 120-meric（120） Consistent with protein copy count Chain A； UniProt 568–850 Chain B； UniProt 70–330 Chain C； UniProt 331–567 Chain D； UniProt 1–69 Fragment：UNP residues 568-850 Fragment：UNP residues 70-330 Fragment：UNP residues 331-567 Fragment：UNP residues 1-69 BT8 3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole × 30 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；298 K；0.4-0.7 M ammonium sulfate, pH 7.5, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.273

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 3VDD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A3R FAB FRAGMENT (ANTIBODY 8F5) COMPLEXED WITH PEPTIDE FROM HUMAN RHINOVIRUS (SEROTYPE 2) VIRAL CAPSID PROTEIN VP2 (RESIDUES 156-170) Deposited 1998-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 225–239（15 aa） Fragment：RESIDUES 156 - 170
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；FAB-PEPTIDE COMPLEX WAS CRYSTALLIZED FROM 0.9 M SODIUM CITRATE, 25 MM SODIUM CHLORIDE, 50 MM TRIS-HCL, PH 7.75, pH 7.5
Resolution 2.10 Å
1CQQ TYPE 2 RHINOVIRUS 3C PROTEASE WITH AG7088 INHIBITOR Deposited 1999-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1687（180 aa）
Not recorded AG7 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；286 K；20% PEG10K, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 13K
Resolution 1.85 Å
1FPN HUMAN RHINOVIRUS SEROTYPE 2 (HRV2) Deposited 2000-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-MERIC
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 60 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；ammonium sulphate, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.60 Å
1FPN HUMAN RHINOVIRUS SEROTYPE 2 (HRV2) Deposited 2000-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；ammonium sulphate, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.60 Å
1FPN HUMAN RHINOVIRUS SEROTYPE 2 (HRV2) Deposited 2000-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；ammonium sulphate, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.60 Å
1FPN HUMAN RHINOVIRUS SEROTYPE 2 (HRV2) Deposited 2000-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；ammonium sulphate, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.60 Å
1FPN HUMAN RHINOVIRUS SEROTYPE 2 (HRV2) Deposited 2000-08-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；ammonium sulphate, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.60 Å
1FPN HUMAN RHINOVIRUS SEROTYPE 2 (HRV2) Deposited 2000-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；ammonium sulphate, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.60 Å
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: complete icosahedral assembly
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 60 CA CALCIUM ION × 60 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 5 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 6 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 150 PDB declaration: 150-meric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Chain 4 2–69（68 aa）
Not recorded DAO LAURIC ACID × 30 CA CALCIUM ION × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.295
2HRV 2A CYSTEINE PROTEINASE FROM HUMAN RHINOVIRUS 2 Deposited 1999-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 851–992（142 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 1.95 Å R-free 0.250
2HRV 2A CYSTEINE PROTEINASE FROM HUMAN RHINOVIRUS 2 Deposited 1999-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 851–992（142 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 1.95 Å R-free 0.250
2XYA Non-covalent inhibtors of rhinovirus 3C protease. Deposited 2010-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1687（180 aa）
Not recorded 7L4 2-PHENYLQUINOLIN-4-OL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.288
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-MERIC
Chain A 568–856（289 aa）
Chain B 70–330（261 aa）
Chain C 331–567（237 aa）
Chain D 2–69（68 aa）
Not recorded DAO LAURIC ACID × 60 CA CALCIUM ION × 60 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 568–856（289 aa）
Chain B 70–330（261 aa）
Chain C 331–567（237 aa）
Chain D 2–69（68 aa）
Not recorded DAO LAURIC ACID × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric
Chain A 568–856（289 aa）
Chain B 70–330（261 aa）
Chain C 331–567（237 aa）
Chain D 2–69（68 aa）
Not recorded DAO LAURIC ACID × 5 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain A 568–856（289 aa）
Chain B 70–330（261 aa）
Chain C 331–567（237 aa）
Chain D 2–69（68 aa）
Not recorded DAO LAURIC ACID × 6 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 568–856（289 aa）
Chain B 70–330（261 aa）
Chain C 331–567（237 aa）
Chain D 2–69（68 aa）
Not recorded DAO LAURIC ACID × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-meric
Chain A 568–856（289 aa）
Chain B 70–330（261 aa）
Chain C 331–567（237 aa）
Chain D 2–69（68 aa）
Not recorded DAO LAURIC ACID × 60 CA CALCIUM ION × 60 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.50 Å R-free 0.441
3TN9 X-ray structure of the HRV2 empty capsid (B-particle) Deposited 2011-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-MERIC
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M sodium acetate pH 6.5 - 8.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.265
3TN9 X-ray structure of the HRV2 empty capsid (B-particle) Deposited 2011-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M sodium acetate pH 6.5 - 8.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.265
3TN9 X-ray structure of the HRV2 empty capsid (B-particle) Deposited 2011-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M sodium acetate pH 6.5 - 8.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.265
3TN9 X-ray structure of the HRV2 empty capsid (B-particle) Deposited 2011-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M sodium acetate pH 6.5 - 8.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.265
3TN9 X-ray structure of the HRV2 empty capsid (B-particle) Deposited 2011-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M sodium acetate pH 6.5 - 8.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.265
3TN9 X-ray structure of the HRV2 empty capsid (B-particle) Deposited 2011-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 45 PDB declaration: 45-meric
Chain 1 568–856（289 aa）
Chain 2 70–330（261 aa）
Chain 3 331–567（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M sodium acetate pH 6.5 - 8.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.265
4L3B X-ray structure of the HRV2 A particle uncoating intermediate Deposited 2013-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-meric
Chain A 568–856（289 aa） Fragment：UNP residues 568-856
Chain B 70–330（261 aa） Fragment：UNP residues 70-330
Chain C 331–567（237 aa） Fragment：UNP residues 331-567
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.5 M ammonium sulfate, 1 M sodium/potassium phosphate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 6.50 Å R-free 0.320
4L3B X-ray structure of the HRV2 A particle uncoating intermediate Deposited 2013-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 568–856（289 aa） Fragment：UNP residues 568-856
Chain B 70–330（261 aa） Fragment：UNP residues 70-330
Chain C 331–567（237 aa） Fragment：UNP residues 331-567
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.5 M ammonium sulfate, 1 M sodium/potassium phosphate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 6.50 Å R-free 0.320
4L3B X-ray structure of the HRV2 A particle uncoating intermediate Deposited 2013-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric
Chain A 568–856（289 aa） Fragment：UNP residues 568-856
Chain B 70–330（261 aa） Fragment：UNP residues 70-330
Chain C 331–567（237 aa） Fragment：UNP residues 331-567
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.5 M ammonium sulfate, 1 M sodium/potassium phosphate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 6.50 Å R-free 0.320
4L3B X-ray structure of the HRV2 A particle uncoating intermediate Deposited 2013-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric
Chain A 568–856（289 aa） Fragment：UNP residues 568-856
Chain B 70–330（261 aa） Fragment：UNP residues 70-330
Chain C 331–567（237 aa） Fragment：UNP residues 331-567
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.5 M ammonium sulfate, 1 M sodium/potassium phosphate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 6.50 Å R-free 0.320
4L3B X-ray structure of the HRV2 A particle uncoating intermediate Deposited 2013-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 568–856（289 aa） Fragment：UNP residues 568-856
Chain B 70–330（261 aa） Fragment：UNP residues 70-330
Chain C 331–567（237 aa） Fragment：UNP residues 331-567
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.5 M ammonium sulfate, 1 M sodium/potassium phosphate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 6.50 Å R-free 0.320
4L3B X-ray structure of the HRV2 A particle uncoating intermediate Deposited 2013-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 45 PDB declaration: 45-meric
Chain A 568–856（289 aa） Fragment：UNP residues 568-856
Chain B 70–330（261 aa） Fragment：UNP residues 70-330
Chain C 331–567（237 aa） Fragment：UNP residues 331-567
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.5 M ammonium sulfate, 1 M sodium/potassium phosphate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 6.50 Å R-free 0.320
5FX5 Novel inhibitors of human rhinovirus 3C protease Deposited 2016-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1687（180 aa） Fragment：3C PROTEASE, RESIDUES 1508-1687
Not recorded GOL GLYCEROL × 2 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 HOV ethyl (4R)-4-[[(2S,3R)-1-[(2S)-3-methyl-2-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]butanoyl]-3-phenyl-pyrrolidin-2-yl]carbonylamino]-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pentanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 30% PEG400, 100 MM TRIS-HCL PH 8.5, 200 MM MGCL2
Resolution 1.70 Å R-free 0.211
5FX6 Novel inhibitors of human rhinovirus 3C protease Deposited 2016-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1687（180 aa） Fragment：3C PROTEASE, RESIDUES 1508-1687
Not recorded 6OY ethyl (4R)-4-[[(2S,4S)-1-[(2S)-3-methyl-2-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]butanoyl]-4-phenyl-pyrrolidin-2-yl]carbonylamino]-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pentanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.2 M CACL2, 0,1 M TRIS PH 8.5, 25% PEG4000
Resolution 1.45 Å R-free 0.186
6FFN Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors Deposited 2018-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1687（180 aa）
Not recorded D8K ~{N}-[(5~{S},8~{S},11~{S},15~{R})-8-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-2,7,10,14-tetrakis(oxidanylidene)-1,6,9,13-tetrazabicyclo[13.3.0]octadecan-11-yl]-5-methyl-1,2-oxazole-3-carboxamide × 1 SO4 SULFATE ION × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；2.0 M Ammonium Sulfate 0.1 M Na Acetate, pH 4.5,
Resolution 1.75 Å R-free 0.170
6FFS Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors Deposited 2018-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1508–1687（180 aa）
Not recorded D8E ~{N}-[(2~{S},5~{S},14~{S})-2-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-9-methyl-3,8,15-tris(oxidanylidene)-1,4,9-triazacyclopentadec-14-yl]-5-methyl-1,2-oxazole-3-carboxamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；2.0 M Ammonium Sulfate 0.1 M Na Acetate, pH 4.5
Resolution 1.86 Å R-free 0.172
7ARA Rhinovirus A2 2A protease in complex with zVAM.fmk Deposited 2020-10-23 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 851–992（142 aa）
Chain B 851–992（142 aa）
Not recorded S7N (phenylmethyl) ~{N}-[(2~{R})-3-methyl-1-[[(2~{S})-1-[[(3~{S})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate × 1 ZN ZINC ION × 2 S7Q (phenylmethyl) ~{N}-[(2~{S})-3-methyl-1-[[(2~{R})-1-[[(3~{R})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；7.5 % PEG8000, 0.3 M KCNS, 5 % 2-methyl-2-butanol, 10 % glycerol, 10 mM b-mercaptoethanol and 50 mM sodium-potassium phosphate buffer pH 8.0
Resolution 2.24 Å R-free 0.257
8AY4 Human rhinovirus 2 virion in situ Deposited 2022-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 240 PDB declaration: 240-meric
Chain A 582–850（269 aa）
Chain B 81–330（250 aa）
Chain C 331–567（237 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
8AY5 Human rhinovirus 2 empty particle in situ Deposited 2022-09-01 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 600–850（251 aa）
Chain B 81–330（250 aa）
Chain C 331–567（237 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
9G0B Rhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius) Deposited 2024-07-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 240 PDB declaration: 240-meric
Chain A 568–850（283 aa）
Chain B 70–330（261 aa）
Chain C 331–567（237 aa）
Chain D 2–69（68 aa）
Not recorded DAO LAURIC ACID × 60 ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8；0.1 M phosphate buffer, pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

17 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HRV2
Isoform —
PDB entities 1, 2, 3, 4
Chains and sequence ranges Author chain A； PDBConstruct 1–283； UniProt 568–850 Author chain B； PDBConstruct 1–261； UniProt 70–330 Author chain C； PDBConstruct 1–237； UniProt 331–567 Author chain D； PDBConstruct 1–69； UniProt 1–69

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 3vdd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3vdd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3vdd
Deposition date deposition_date2012-01-05
Structure title titleStructure of HRV2 capsid complexed with antiviral compound BTA798
Keywords keywordsviral capsid, virus-drug complex, VIRUS; VIRUS
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_guinier29.12 Å
Radius of gyration Rg (electron density) rg_electron28.30 Å
Forward intensity I(0) i0131447000.00
Molecular weight molecular_weight90342.0 kDa
Excluded volume excluded_volume112790 ų
Envelope volume envelope_volume138670 ų
Hydration-shell volume shell_volume39857 ų
Envelope diameter envelope_diameter101.2 Å
Shell Rg shell_rg36.36 Å
Envelope Rg envelope_rg28.89 Å
Shape Rg shape_rg28.29 Å
Total Rg total_rg29.08 Å
Total atoms total_atoms6368
Residues n_residues804
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 dmax93.1 Å
Rg (real space) rg_real29.06 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real1.3140e+08
I(0) uncertainty (real space) i0_real_error2.0570e+06
Rg (reciprocal space) rg_reciprocal29.09 Å
I(0) (reciprocal space) i0_reciprocal131400000.0000
Solution quality estimate total_estimate0.8883
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.5 Å
Skewness Skewness skewness0.319
Kurtosis Kurtosis kurtosis-0.271
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30110000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.875
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3vddA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3vddB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3vddC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)