SAXSdb — 2l45

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

C-TERMINAL ZINC KNUCLE OF THE HIV-NCP7

OrganismNot specified

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 411–429	Not recorded	;DNA (5'-D(PTPAPCPGPCPC)-3') ; × 1 ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions：pH 5.7；298 K；Ionic strength (raw mmCIF value) 6.0；Pressure ambient NMR sample composition：1 mM C-terminal zinc knuckle of the HIVNCp7, 1 mM DNA, 90% H2O/10% D2O \| 90% H2O/10% D2O	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.

Other PDB	Difference from Current Entry 2L45	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L44 C-terminal zinc knuckle of the HIVNCp7 Deposited 2010-10-01	Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 411–429（19 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 5.7；298 K；Ionic strength (raw mmCIF value) 6；Pressure ambient NMR sample composition 1 mM C-terminal zinc knuckle of the HIVNCp7, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L46 C-terminal zinc finger of the HIVNCp7 with platinated DNA Deposited 2010-10-01	Parsed fields agree	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 411–429（19 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 5.7；298 K；Ionic strength (raw mmCIF value) 6.0；Pressure ambient NMR sample composition 1 mM C-terminal zinc knuckle of the HIVNCp7, 1 mM DNA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3OUA MDR769 HIV-1 protease complexed with p1/p6 hepta-peptide Deposited 2010-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 446–452（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 01 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.226
3OUC MDR769 HIV-1 protease complexed with p2/NC hepta-peptide Deposited 2010-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 375–381（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；0.8M NaCl 0.1 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.262
3P9G Crystal structure of the TSG101 UEV domain in complex with FA459 peptide Deposited 2010-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 453–461（9 aa） Fragment：Modified HIV-1 Gag PTAP Motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M HEPES-NAOH (PH7.5), 25% PEG 3350, 0.2M SODIUM NITRATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.242
3P9H Crystal structure of the TSG101 UEV domain in complex with FA258 peptide Deposited 2010-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 453–461（9 aa） Fragment：Modified HIV-1 Gag PTAP Motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M HEPES-NAOH (PH7.5), 25% PEG 3350, 0.2M SODIUM NITRATE , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.253
4EP3 Crystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate CA-p2 Deposited 2012-04-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 359–367（9 aa）	Not recorded	GOL GLYCEROL × 3 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.81 Å R-free 0.227
4EPJ Crystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate p2-NC Deposited 2012-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 374–381（8 aa）	Not recorded	GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 1 ACT ACETATE ION × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.69 Å R-free 0.227
4EQ0 Crystal Structure of inactive single chain variant of HIV-1 Protease in Complex with the substrate p2-NC Deposited 2012-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 374–381（8 aa）	Not recorded	BME BETA-MERCAPTOETHANOL × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 3 ACT ACETATE ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；295 K；126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.70 Å R-free 0.264
4FAE Substrate p2/NC in Complex with a Human Immunodeficiency Virus Type 1 Protease Variant Deposited 2012-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 375–381（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；0.1 M citric acid, 2.4 M ammonium sulfate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.279

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9YP46_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–19； UniProt 411–429

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	2l45
Deposition date deposition_date	2010-10-01
Structure title title	C-terminal zinc knuckle of the HIVNCp7 with DNA
Keywords keywords	NCP7, HIV, Platinum, 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	9.12 Å
Radius of gyration Rg (electron density) rg_electron	9.15 Å
Forward intensity I(0) i0	160912000.00
Molecular weight molecular_weight	76916.0 kDa
Excluded volume excluded_volume	83866 Å³
Envelope volume envelope_volume	9525 Å³
Hydration-shell volume shell_volume	7687 Å³
Envelope diameter envelope_diameter	38.5 Å
Shell Rg shell_rg	16.26 Å
Envelope Rg envelope_rg	11.53 Å
Shape Rg shape_rg	9.19 Å
Total Rg total_rg	9.27 Å
Total atoms total_atoms	9196
Residues n_residues	475
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	35.1 Å
Rg (real space) rg_real	9.11 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.6090e+08
I(0) uncertainty (real space) i0_real_error	2.2760e+06
Rg (reciprocal space) rg_reciprocal	9.11 Å
I(0) (reciprocal space) i0_reciprocal	160900000.0000
Solution quality estimate total_estimate	0.8134
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	10.7 Å
Skewness Skewness skewness	0.325
Kurtosis Kurtosis kurtosis	-0.221
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35970.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.606; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.758; Smooth: 0.996

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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	C-TERMINAL ZINC KNUCLE OF THE HIV-NCP7
Molecular weight formula_weight	2230.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9196

KGCWKCGKEGHQMKDCTER

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PTPAPCPGPCPC)-3') ;
Molecular weight formula_weight	1769.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

TACGCC

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	1

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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/l4/2l45/2l45.fit
pddf	/app/data/pr_computation/l4/2l45/2l45.pr.out
profile	/app/data/saxs_computation/l4/2l45/2l45.dat

C-terminal zinc knuckle of the HIVNCp7 with DNA

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

C-TERMINAL ZINC KNUCLE OF THE HIV-NCP7

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

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)