SAXSdb — 1d4m

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

PROTEIN (COXSACKIEVIRUS A9)

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	5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 120 MYRISTIC ACID × 60 water × 240	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 2 MYRISTIC ACID × 1 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 20	5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 10 MYRISTIC ACID × 5 water × 20	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 24	5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 12 MYRISTIC ACID × 6 water × 24	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 2 MYRISTIC ACID × 1 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 120	5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE × 60 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_CXA9
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain 1； PDBConstruct 1–299； UniProt 568–866 Author chain 2； PDBConstruct 1–261； UniProt 69–329 Author chain 3； PDBConstruct 1–238； UniProt 330–567 Author chain 4； PDBConstruct 1–68； UniProt 1–68

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	1d4m
Deposition date deposition_date	1999-10-04
Structure title title	THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION
Keywords keywords	PICORNAVIRUS STRUCTURE, RGD, UNCOATING, VIRUS-RECEPTOR INTERACTION, WIN COMPOUND, VIRUS/VIRAL PROTEIN, Icosahedral virus, Virus; 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.

1d4m__assembly_1__model_1

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

Download this curve (.dat)

1d4m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1d4m__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)	132.40 Å
Total Rg	132.40 Å
Atom count	396180
Residues	50100
Excluded volume	7026500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1d4m__assembly_1__model_1`	240-MERIC （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1d4m__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1d4m__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1d4m__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1d4m__assembly_5__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`1d4m__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 (7)

Entity 1 Entity 1 polymer

Description description	PROTEIN (COXSACKIEVIRUS A9)
Molecular weight formula_weight	33869.0 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	7051

GDVEEAIERAVVHVADTMRSGPSNSASVPALTAVETGHTSQVTPSDTMQTRHVKNYHSRSESTVENFLGRSACVYMEEYKTTDNDVNKKFVAWPINTKQMVQMRRKLEMFTYLRFDMEVTFVITSRQDPGTTLAQDMPVLTHQIMYVPPGGPIPAKVDDYAWQTSTNPSIFWTEGNAPARMSIPFISIGNAYSNFYDGWSNFDQRGSYGYNTLNNLGHIYVRHVSGSSPHPITSTIRVYFKPKHTRAWVPRPPRLCQYKKAFSVDFTPTPITDTRKDINTVTTVAQSRRRGDMSTLNTH

Entity 2 Entity 2 polymer

Description description	PROTEIN (COXSACKIEVIRUS A9)
Molecular weight formula_weight	28885.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

SPTVEECGYSDRVRSITLGNSTITTQECANVVVGYGRWPTYLRDDEATAEDQPTQPDVATCRFYTLDSIKWEKGSVGWWWKFPEALSDMGLFGQNMQYHYLGRAGYTIHVQCNASKFHQGCLLVVCVPEAEMGGAVVGQAFSATAMANGDKAYEFTSATQSDQTKVQTAIHNAGMGVGVGNLTIYPHQWINLRTNNSATIVMPYINSVPMDNMFRHYNFTLMVIPFVKLDYADTASTYVPITVTVAPMCAEYNGLRLAQAQ

Entity 3 Entity 3 polymer

Description description	PROTEIN (COXSACKIEVIRUS A9)
Molecular weight formula_weight	26335.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

GLPTMNTPGSTQFLTSDDFQSPCALPQFDVTPSMNIPGEVKNLMEIAEVDSVVPVNNVQDTTDQMEMFRIPVTINAPLQQQVFGLRLQPGLDSVFKHTLLGEILNYYAHWSGSMKLTFVFCGSAMATGKFLIAYSPPGANPPKTRKDAMLGTHIIWDIGLQSSCVLCVPWISQTHYRLVQQDEYTSAGYVTCWYQTGMIVPPGTPNSSSIMCFASACNDFSVRMLRDTPFISQDNKLQ

Entity 4 Entity 4 polymer

Description description	PROTEIN (COXSACKIEVIRUS A9)
Molecular weight formula_weight	7352.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4

GAQVSTQKTGAHETSLSAAGNSIIHYTNINYYKDAASNSANRQDFTQDPSKFTEPVKDVMIKSLPALN

Entity 5 Entity 5 non-polymer

Description description	5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE
Molecular weight formula_weight	342.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	448

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1d4m.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	d1d4m1_
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	d1d4m3_
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 (4 domains)

Domain ID domain_id	1d4m100
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1d4m200
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1d4m300
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1d4m400
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	10 — Picornavirus coat protein VP4

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Unit-cell length a length_a	487.300 Å
Unit-cell length b length_b	358.100 Å
Unit-cell length c length_c	305.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	128.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	120

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1690
R_work r_work	0.1690
R_free r_free	—

THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION

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

PROTEIN (COXSACKIEVIRUS A9)

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

1d4m__assembly_1__model_1

1d4m__assembly_1__model_1 | I(q)

1d4m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

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 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (2)

THE CRYSTAL STRUCTURE OF COXSACKIEVIRUS A9 TO 2.9 A RESOLUTION

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

PROTEIN (COXSACKIEVIRUS A9)

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

1d4m__assembly_1__model_1

1d4m__assembly_1__model_1 | I(q)

1d4m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (7)

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 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (2)