SAXSdb — 5vxr

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

MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain

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 H； UniProt 141–239	Not recorded	MAb24 Variable Light Chain,MAb24 Variable Light Chain × 1 （A0A125T908） Virus Envelope Protein 2 × 1 （Q5EG65） 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

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 5VXR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5IKC X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB Deposited 2016-03-03	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 B 21–240（220 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；unknown	Resolution 2.06 Å R-free 0.265
5IKC X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB Deposited 2016-03-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 21–240（220 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；unknown	Resolution 2.06 Å R-free 0.265
6U2F PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)IGLLR - NH2 Deposited 2019-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 137–239（103 aa） Fragment：Fab	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；291 K；4 M ammonium acetate, 0.1 M Tris, pH 8.5, 3% v/v 1,8 diaminooctane	Resolution 2.94 Å R-free 0.209

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q569X1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 119–217； UniProt 141–239

MAb24 Variable Light Chain,MAb24 Variable Light Chain

OrganismNot specified

UniProt A0A125T908

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 L； UniProt 131–237	Not recorded	MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain × 1 （Q569X1） Virus Envelope Protein 2 × 1 （Q5EG65） 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

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	A0A125T908_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 111–217； UniProt 131–237

Virus Envelope Protein 2

OrganismNot specified

UniProt Q5EG65

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：Epitope I (UNP residues 412-423)	MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain × 1 （Q569X1） MAb24 Variable Light Chain,MAb24 Variable Light Chain × 1 （A0A125T908） 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

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 5VXR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GAG Structure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 412-423) Deposited 2012-07-25	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：Residues 412-423 of HCV E2	Non-standard monomer：Yes (specific site not provided by mmCIF)	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

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	5vxr
Deposition date deposition_date	2017-05-24
Structure title title	The antigen-binding fragment of MAb24 in complex with a peptide from Hepatitis C Virus E2 epitope I (412-423)
Keywords keywords	Antibody, 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	25.37 Å
Radius of gyration Rg (electron density) rg_electron	24.35 Å
Forward intensity I(0) i0	39800600.00
Molecular weight molecular_weight	48062.0 kDa
Excluded volume excluded_volume	59747 Å³
Envelope volume envelope_volume	72394 Å³
Hydration-shell volume shell_volume	24926 Å³
Envelope diameter envelope_diameter	84.3 Å
Shell Rg shell_rg	31.32 Å
Envelope Rg envelope_rg	24.30 Å
Shape Rg shape_rg	24.34 Å
Total Rg total_rg	25.14 Å
Total atoms total_atoms	6639
Residues n_residues	430
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	81.7 Å
Rg (real space) rg_real	25.37 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	3.9800e+07
I(0) uncertainty (real space) i0_real_error	5.8060e+05
Rg (reciprocal space) rg_reciprocal	25.37 Å
I(0) (reciprocal space) i0_reciprocal	39800000.0000
Solution quality estimate total_estimate	0.9024
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.304
Kurtosis Kurtosis kurtosis	-0.511
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8315000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.981

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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	MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain
Molecular weight formula_weight	23160.7 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	7192

VQLQESGPSLVKPSQTLSLTCSVTGDSITSGYWNWIRKFPGNKLEYVGYISYSGDTYYNPSLKSRISITRDTSKNQYYLQLNSVTSEDTATYYCARMGYGSQPGFGSWGQGTLVTVSAAKTTPPSVYPLAPGSGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP

Entity 2 Entity 2 polymer

Description description	MAb24 Variable Light Chain,MAb24 Variable Light Chain
Molecular weight formula_weight	23906.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

NIVLTQSPVSLAVSLGQRATISCRASESVDSYGKSFLHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQHNNEDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERNNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRND

Entity 3 Entity 3 polymer

Description description	Virus Envelope Protein 2
Molecular weight formula_weight	1383.5 kDa
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	11

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	447

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5vxrH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vxrL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vxrL02
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	70.370 Å
Unit-cell length b length_b	53.338 Å
Unit-cell length c length_c	133.903 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	14.110 Å
R factor r_factor	0.1720
R_work r_work	0.1710
R_free r_free	0.1900

fit	/app/data/saxs_computation/vx/5vxr/5vxr.fit
pddf	/app/data/pr_computation/vx/5vxr/5vxr.pr.out
profile	/app/data/saxs_computation/vx/5vxr/5vxr.dat

The antigen-binding fragment of MAb24 in complex with a peptide from Hepatitis C Virus E2 epitope I (412-423)

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

MAb24 Variable Heavy Chain,MAb24 Variable Heavy Chain

State in the Current Structure

Other States of the Same Protein in the Database

MAb24 Variable Light Chain,MAb24 Variable Light Chain

State in the Current Structure

Other States of the Same Protein in the Database

Virus Envelope Protein 2

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) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)