SAXSdb — 4gag

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

Genome polyprotein

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain P； UniProt 412–423	Fragment：Residues 412-423 of HCV E2 Non-standard monomer：Yes (specific site not provided by mmCIF)	NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN × 1 NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；18% PEG 8K, 0.1M TrisHCl, 0.2M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.211

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 4GAG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5VXR The antigen-binding fragment of MAb24 in complex with a peptide from Hepatitis C Virus E2 epitope I (412-423) Deposited 2017-05-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 412–423（12 aa） Fragment：Epitope I (UNP residues 412-423)	Not recorded	GOL GLYCEROL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；12.5% PEG3000, 100 mM sodium chloride, 100 mM sodium phosphate dibasic/citric acid, pH 6.2	Resolution 1.40 Å R-free 0.190

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POLG_HCVGL
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–12； UniProt 412–423

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	4gag
Deposition date deposition_date	2012-07-25
Structure title title	Structure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 412-423)
Keywords keywords	antibody Fab, neutralizing antibody, HCV E2 binding, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	25.20 Å
Radius of gyration Rg (electron density) rg_electron	24.20 Å
Forward intensity I(0) i0	39735000.00
Molecular weight molecular_weight	48215.0 kDa
Excluded volume excluded_volume	60030 Å³
Envelope volume envelope_volume	72759 Å³
Hydration-shell volume shell_volume	25292 Å³
Envelope diameter envelope_diameter	85.4 Å
Shell Rg shell_rg	31.15 Å
Envelope Rg envelope_rg	23.99 Å
Shape Rg shape_rg	24.19 Å
Total Rg total_rg	25.02 Å
Total atoms total_atoms	3396
Residues n_residues	429
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	82.8 Å
Rg (real space) rg_real	25.18 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	3.9730e+07
I(0) uncertainty (real space) i0_real_error	5.2520e+05
Rg (reciprocal space) rg_reciprocal	25.19 Å
I(0) (reciprocal space) i0_reciprocal	39740000.0000
Solution quality estimate total_estimate	0.8983
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.289
Kurtosis Kurtosis kurtosis	-0.476
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9172000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
Molecular weight formula_weight	23677.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	3770

EVQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYMGYISYSGSTYYNLSLRSRISITRDTSKNQYYLQLNSVTTEDTATYYCALITTTTYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Entity 2 Entity 2 polymer

Description description	NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN
Molecular weight formula_weight	23921.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

NIVLTQSPVSLAVSLGQRATISCRASESVDGYGNSFLHWFQQKPGQPPKLLIYLASNLNSGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNVDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 3 Entity 3 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	1366.5 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

QLINTNGSWHVN

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	346

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4gagH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4gagH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4gagL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4gagL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	127.649 Å
Unit-cell length b length_b	56.903 Å
Unit-cell length c length_c	81.802 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	23.110 Å
R factor r_factor	0.1794
R_work r_work	0.1777
R_free r_free	0.2109

fit	/app/data/saxs_computation/ga/4gag/4gag.fit
pddf	/app/data/pr_computation/ga/4gag/4gag.pr.out
profile	/app/data/saxs_computation/ga/4gag/4gag.dat

Structure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 412-423)

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

Genome polyprotein

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)