SAXSdb — 4qnb

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

CAPSID PROTEIN P24

Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1N5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–231； UniProt 133–363

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	4qnb
Deposition date deposition_date	2014-06-17
Structure title title	Disulfide stabilized HIV-1 CA hexamer in complex with PHENYL-L-PHENYLALANINAMIDE inhibitor
Keywords keywords	capsid protein, disulfide crosslink, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex; VIRAL PROTEIN/INHIBITOR
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.

4qnb__assembly_1__model_1

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

Download this curve (.dat)

4qnb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4qnb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.17 Å
Rg (electron density)	35.30 Å
Total Rg	35.79 Å
Atom count	10326
Residues	1290
Excluded volume	181330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4qnb__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	CAPSID PROTEIN P24
Molecular weight formula_weight	25461.3 kDa
Mutation mutation	A14C,E45C,W184A,M185A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1821

PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Source Source

Source organism organism	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11698
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE
Molecular weight formula_weight	425.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4qnba1
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

Domain ID domain_id	d4qnba2
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

CATH v4.4 (2 domains)

Domain ID domain_id	4qnbA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

Domain ID domain_id	4qnbA02
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	91.383 Å
Unit-cell length b length_b	91.383 Å
Unit-cell length c length_c	56.587 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	6

Space group space_group	P 6
Space-group number int_tables_number	168
Crystal system crystal_system	—

Resolution resolution	1.996 Å
Low-resolution limit resolution_low	26.642 Å
R factor r_factor	0.2227
R_work r_work	0.2203
R_free r_free	0.2707

Disulfide stabilized HIV-1 CA hexamer in complex with PHENYL-L-PHENYLALANINAMIDE inhibitor

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

CAPSID PROTEIN P24

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

4qnb__assembly_1__model_1

4qnb__assembly_1__model_1 | I(q)

4qnb__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Disulfide stabilized HIV-1 CA hexamer in complex with PHENYL-L-PHENYLALANINAMIDE inhibitor

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

CAPSID PROTEIN P24

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

4qnb__assembly_1__model_1

4qnb__assembly_1__model_1 | I(q)

4qnb__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)