SAXSdb — 1bj6

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

NUCLEOCAPSID PROTEIN 7

Human immunodeficiency virus 1

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–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 390–430	Fragment：RESIDUES 12-53	;DNA (5'-D(APCPGPCP*C)-3') ; × 1 ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions：pH 6；303 K；Ionic strength (raw mmCIF value) LOW SALT CONDITIONS；Pressure 1 NMR sample composition：WATER	Resolution not provided

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q74084_9HIV1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 2–42； UniProt 390–430

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	1bj6
Deposition date deposition_date	1998-07-03
Structure title title	1H NMR OF (12-53) NCP7/D(ACGCC) COMPLEX, 10 STRUCTURES
Keywords keywords	COMPLEX (NUCLEOCAPSID PROTEIN-DNA), NUCLEIC ACID, RETROVIRUS, VIRUS MORPHOGENESIS, ZINC FINGER, Viral protein-DNA COMPLEX; Viral protein/DNA
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	11.35 Å
Radius of gyration Rg (electron density) rg_electron	11.28 Å
Forward intensity I(0) i0	100534000.00
Molecular weight molecular_weight	64134.0 kDa
Excluded volume excluded_volume	72397 Å³
Envelope volume envelope_volume	14427 Å³
Hydration-shell volume shell_volume	9750 Å³
Envelope diameter envelope_diameter	46.5 Å
Shell Rg shell_rg	18.31 Å
Envelope Rg envelope_rg	13.57 Å
Shape Rg shape_rg	11.28 Å
Total Rg total_rg	11.56 Å
Total atoms total_atoms	8100
Residues n_residues	470
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	41.3 Å
Rg (real space) rg_real	11.38 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.0050e+08
I(0) uncertainty (real space) i0_real_error	1.2130e+06
Rg (reciprocal space) rg_reciprocal	11.38 Å
I(0) (reciprocal space) i0_reciprocal	100500000.0000
Solution quality estimate total_estimate	0.7681
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	12.0 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.248
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	71590.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.742; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(APCPGPCP*C)-3') ;
Molecular weight formula_weight	1465.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	8100

ACGCC

Entity 2 Entity 2 polymer

Description description	NUCLEOCAPSID PROTEIN 7
Molecular weight formula_weight	4837.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQ

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI Class编号 ncbi_taxonomy_id	11676

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bj6a_
Class class	g — Small proteins
Fold Fold fold	g.40 — Retrovirus zinc finger-like domains
Superfamily Superfamily superfamily	g.40.1 — Retrovirus zinc finger-like domains
Family Family family	g.40.1.1 — Retrovirus zinc finger-like domains

CATH v4.4 (1 domains)

Domain ID domain_id	1bj6A00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	60 — HIV-1 Nucleocapsid Protein
Homologous superfamily homologous superfamily	10 — Zinc finger, CCHC-type

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

fit	/app/data/saxs_computation/bj/1bj6/1bj6.fit
pddf	/app/data/pr_computation/bj/1bj6/1bj6.pr.out
profile	/app/data/saxs_computation/bj/1bj6/1bj6.dat

1H NMR OF (12-53) NCP7/D(ACGCC) COMPLEX, 10 STRUCTURES

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

NUCLEOCAPSID PROTEIN 7

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)