SAXSdb — 5dck

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

Capsid C-Terminal Domain

Feline immunodeficiency virus (isolate Petaluma)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GAG_FIVPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–72； UniProt 278–347 Author chain B； PDBConstruct 3–72； UniProt 278–347

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	5dck
Deposition date deposition_date	2015-08-24
Structure title title	Crystal Structure of FIV Capsid C-Terminal Domain
Keywords keywords	Retrovirus, FIV, Capsid, viral protein; VIRAL PROTEIN
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.

5dck__assembly_1__model_1

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

Download this curve (.dat)

5dck__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dck__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.46 Å
Rg (electron density)	15.30 Å
Total Rg	16.44 Å
Atom count	1141
Residues	143
Excluded volume	20197 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dck__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5dcka1
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.3 — Retrovirus capsid dimerization domain-like
Family Family family	a.28.3.0 — automated matches

Domain ID domain_id	d5dcka2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5dckb1
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.3 — Retrovirus capsid dimerization domain-like
Family Family family	a.28.3.0 — automated matches

Domain ID domain_id	d5dckb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5dckA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	30 — Retrovirus capsid C-terminal domain

Domain ID domain_id	5dckB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	30 — Retrovirus capsid C-terminal domain

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Unit-cell length a length_a	64.190 Å
Unit-cell length b length_b	64.190 Å
Unit-cell length c length_c	178.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	40.630 Å
R factor r_factor	0.2378
R_work r_work	0.2353
R_free r_free	0.2868

Description description	Capsid C-Terminal Domain
Molecular weight formula_weight	8253.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1239

Crystal Structure of FIV Capsid C-Terminal Domain

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

Capsid C-Terminal Domain

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

5dck__assembly_1__model_1

5dck__assembly_1__model_1 | I(q)

5dck__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Feline immunodeficiency virus (isolate Petaluma)
Common name common_name	FIV
NCBI taxonomy ID ncbi_taxonomy_id	11674
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

Crystal Structure of FIV Capsid C-Terminal Domain

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

Capsid C-Terminal Domain

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

5dck__assembly_1__model_1

5dck__assembly_1__model_1 | I(q)

5dck__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)