1qju

HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP61209

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN VP1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 240	ZINC ION × 60 2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2N-METHYL-2H-TETRAZOL-5-YL]-PHENOL × 60 MYRISTIC ACID × 60 water × 240	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 1 2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2N-METHYL-2H-TETRAZOL-5-YL]-PHENOL × 1 MYRISTIC ACID × 1 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 20	ZINC ION × 5 2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2N-METHYL-2H-TETRAZOL-5-YL]-PHENOL × 5 MYRISTIC ACID × 5 water × 20	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 24	ZINC ION × 6 2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2N-METHYL-2H-TETRAZOL-5-YL]-PHENOL × 6 MYRISTIC ACID × 6 water × 24	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 1 2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2N-METHYL-2H-TETRAZOL-5-YL]-PHENOL × 1 MYRISTIC ACID × 1 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 120	ZINC ION × 30 2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2N-METHYL-2H-TETRAZOL-5-YL]-PHENOL × 30 MYRISTIC ACID × 30 water × 120	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_HRV16
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain 1； PDBConstruct 1–285； UniProt 569–853 Author chain 2； PDBConstruct 1–261； UniProt 70–330 Author chain 3； PDBConstruct 1–238； UniProt 331–568 Author chain 4； PDBConstruct 1–68； UniProt 2–69

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1qju
Deposition date deposition_date	1999-07-05
Structure title title	HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP61209
Keywords keywords	;VIRUS, NUCLEOTIDYLTRANSFERASE, RHINOVIRUS COAT PROTEIN, RNA-BINDING, TRANSFERASE, LIPOPROTEIN, WIN COMPOUND, PHOSPHOPROTEIN, THIOL PROTEASE, CAPSID PROTEIN, DRUG, VIRION, MEMBRANE, HELICASE, PROTEASE, NUCLEOTIDE-BINDING, HUMAN RHINOVIRUS 16, RNA REPLICATION, ANTIVIRAL COMPOUND, COVALENT PROTEIN-RNA LINKAGE, MYRISTATE, HYDROLASE, CYTOPLASM, ATP-BINDING, CYTOPLASMIC VESICLE, HOST-VIRUS INTERACTION, RNA-DIRECTED RNA POLYMERASE ;; VIRUS
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1qju__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1qju__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1qju__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	0.00 Å
Rg (electron density)	132.10 Å
Total Rg	132.20 Å
Atom count	382524
Residues	48240
Excluded volume	6784800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1qju__assembly_1__model_1`	240-MERIC （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1qju__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1qju__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1qju__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1qju__assembly_5__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`1qju__assembly_6__model_1`	120-meric （120）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	PROTEIN VP1
Molecular weight formula_weight	32501.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1
Atom count atom_count	6719

NPVERYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQTLDEMSVESFLGRSGCIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGHIVMQYMYVPPGAPIPTTRDDYAWQSGTNASVFWQHGQPFPRFSLPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSEQLHKVKVVTRIYHKAKHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV

Entity 2 Entity 2 polymer

Description description	PROTEIN VP2
Molecular weight formula_weight	28990.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

SPSVEACGYSDRIIQITRGDSTITSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLDSKMWNSTSKGWWWKLPDALKDMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLLVVMIPEHQLATVNKGNVNAGYKYTHPGEAGREVGTQVENEKQPSDDNWLNFDGTLLGNLLIFPHQFINLRSNNSATLIVPYVNAVPMDSMVRHNNWSLVIIPVCQLQSNNISNIVPITVSISPMCAEFSGARAKTVVQ

Entity 3 Entity 3 polymer

Description description	PROTEIN VP3
Molecular weight formula_weight	26314.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

GLPVYVTPGSGQFMTTDDMQSPCALPWYHPTKEIFIPGEVKNLIEMCQVDTLIPINSTQSNIGNVSMYTVTLSPQTKLAEEIFAIKVDIASHPLATTLIGEIASYFTHWTGSLRFSFMFCGTANTTLKVLLAYTPPGIGKPRSRKEAMLGTHVVWDVGLQSTVSLVVPWISASQYRFTTPDTYSSAGYITCWYQTNFVVPPNTPNTAEMLCFVSGCKDFCLRMARDTDLHKQTGPITQ

Entity 4 Entity 4 polymer

Description description	PROTEIN VP4
Molecular weight formula_weight	7374.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4

GAQVSRQNVGTHSTQNMVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2N-METHYL-2H-TETRAZOL-5-YL]-PHENOL
Molecular weight formula_weight	327.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1qju.1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Domain ID domain_id	d1qju1_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Domain ID domain_id	d1qju3_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

CATH v4.4 (3 domains)

Domain ID domain_id	1qju100
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1qju200
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1qju300
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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7. Citations (8)

Analysis of Three Structurally Related Antiviral Compounds in Complex with Human Rhinovirus 16

Proc.Natl.Acad.Sci.USA (1999)

PMID: 10611281 · DOI: 10.1073/PNAS.96.26.14730 PRIMARY

The Refined Structure of Human Rhinovirus 16 at 2.15 Angstroms Resolution: Implications for the Viral Life Cycle

Structure (1997)

PMID: 9083115 · DOI: 10.1016/S0969-2126(97)00199-8

The Structure of Human Rhinovirus 16

Structure (1993)

PMID: 7915182 · DOI: 10.1016/0969-2126(93)90008-5

Structure of a Human Rhinovirus Complexed with its Receptor Molecule

Proc.Natl.Acad.Sci.USA (1993)

PMID: 8093643 · DOI: 10.1073/PNAS.90.2.507

A Comparison of the Anti-Rhinoviral Drug Binding Pocket in Hrv14 and Hrv1A

J.Mol.Biol. (1993)

PMID: 8383771 · DOI: 10.1006/JMBI.1993.1137

Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)

J.Mol.Biol. (1989)

PMID: 2555523 · DOI: 10.1016/0022-2836(89)90293-3

The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating

Science (1986)

PMID: 3018924 · DOI: 10.1126/SCIENCE.3018924

Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses

Nature (1985)

PMID: 2993920 · DOI: 10.1038/317145A0

Unit-cell length a length_a	362.600 Å
Unit-cell length b length_b	347.100 Å
Unit-cell length c length_c	334.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	120

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2120

HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP61209

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN VP1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1qju__assembly_1__model_1

1qju__assembly_1__model_1 | I(q)

1qju__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (8)

HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP61209

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN VP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1qju__assembly_1__model_1

1qju__assembly_1__model_1 | I(q)

1qju__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (8)