SAXSdb — 5tr8

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

441D6 Fab Light chain

Mus musculus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 132–234	Not recorded	441D6 Fab Heavy chain × 1 （A0A0E4B366） NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；273 K；12% PEG3350, 100 mM HEPES pH 7.5, 5 mM MgCl2, 5mM NiCl2	Resolution 2.01 Å R-free 0.198

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 5TR8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D5B UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104) Chain L 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.285
1D5B UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.285
1D5B UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.285
1D5I UNLIGANDED GERMLINE PRECURSOR OF AN OXY-COPE CATALYTIC ANTIBODY Deposited 1999-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)	Not recorded	CD CADMIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；75mM Hepes pH 7.0 9% PEG 4000 150 mM Ammonium Sulfate 20% 1,4 butanediol 100 mM Cadmium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.263
1D6V CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-COPE ANTIBODY MATURATION Deposited 1999-10-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 23–129（107 aa） Fragment：chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)	Not recorded	CD CADMIUM ION × 4 HOP (1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；9% polyethylene glycol 4000 250mM ammonium sulfate 80mM Cadmium Chloride 75mM Hepes 20% 1,4 butanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 19K	Resolution 2.00 Å R-free 0.264
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 720 PDB declaration: 720-meric	Chain H 130–234（105 aa） Fragment：SEE REMARK 999 Chain J 130–234（105 aa） Fragment：SEE REMARK 999 Chain L 130–234（105 aa） Fragment：SEE REMARK 999	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 130–234（105 aa） Fragment：SEE REMARK 999 Chain J 130–234（105 aa） Fragment：SEE REMARK 999 Chain L 130–234（105 aa） Fragment：SEE REMARK 999	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 60 PDB declaration: 60-meric	Chain H 130–234（105 aa） Fragment：SEE REMARK 999 Chain J 130–234（105 aa） Fragment：SEE REMARK 999 Chain L 130–234（105 aa） Fragment：SEE REMARK 999	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Heteromer；Protein × 72 PDB declaration: 72-meric	Chain H 130–234（105 aa） Fragment：SEE REMARK 999 Chain J 130–234（105 aa） Fragment：SEE REMARK 999 Chain L 130–234（105 aa） Fragment：SEE REMARK 999	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 130–234（105 aa） Fragment：SEE REMARK 999 Chain J 130–234（105 aa） Fragment：SEE REMARK 999 Chain L 130–234（105 aa） Fragment：SEE REMARK 999	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
4KVC 2H2 Fab fragment of immature Dengue virus Deposited 2013-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 130–234（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；25% PEG 6000 0.1 M MES 0.2M NH4Cl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.31 Å R-free 0.234
5VPL CRYSTAL STRUCTURE OF DER F 1 COMPLEXED WITH FAB 4C1 Deposited 2017-05-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 24–235（212 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.1M HEPES, 18% W/V PEG12K, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.90 Å R-free 0.194

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q7TS98_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 110–212； UniProt 132–234

441D6 Fab Heavy chain

Mus musculus

UniProt A0A0E4B366

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 133–239	Not recorded	441D6 Fab Light chain × 1 （Q7TS98） NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；273 K；12% PEG3350, 100 mM HEPES pH 7.5, 5 mM MgCl2, 5mM NiCl2	Resolution 2.01 Å R-free 0.198

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	A0A0E4B366_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 115–221； UniProt 133–239

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	5tr8
Deposition date deposition_date	2016-10-25
Structure title title	Crystal structure of vaccine-elicited pan- influenza H1N1 neutralizing murine antibody 441D6.
Keywords keywords	Nanoparticle, Ferritin, Immune system, Antibody; 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	25.78 Å
Radius of gyration Rg (electron density) rg_electron	24.70 Å
Forward intensity I(0) i0	39273300.00
Molecular weight molecular_weight	47511.0 kDa
Excluded volume excluded_volume	58947 Å³
Envelope volume envelope_volume	73806 Å³
Hydration-shell volume shell_volume	25042 Å³
Envelope diameter envelope_diameter	81.4 Å
Shell Rg shell_rg	31.89 Å
Envelope Rg envelope_rg	24.46 Å
Shape Rg shape_rg	24.70 Å
Total Rg total_rg	25.51 Å
Total atoms total_atoms	3337
Residues n_residues	426
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	80.8 Å
Rg (real space) rg_real	25.75 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	3.9270e+07
I(0) uncertainty (real space) i0_real_error	5.3680e+05
Rg (reciprocal space) rg_reciprocal	25.76 Å
I(0) (reciprocal space) i0_reciprocal	39270000.0000
Solution quality estimate total_estimate	0.9090
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.261
Kurtosis Kurtosis kurtosis	-0.562
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7126000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.940

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	441D6 Fab Light chain
Molecular weight formula_weight	23694.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3585

DIKMTQSPSSMYASLGERVTFTCKASQDIYSSFSWFQQRPGKSPKTLIYRANRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGVYFCLQHEEFPPTFGGGTKLELKRTDAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	441D6 Fab Heavy chain
Molecular weight formula_weight	23879.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLVESGGGLMRPGGSLKLSCAASGFAFSRFDMSWVRQTPEKRLEWVAYIRNGADDTYYADTEKGRFTISRDNAKNTLYLQLSSLKIEDTAMYYCVRHSGYSYVIDYWGQGTSVTVSSASTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPRVP

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	248

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5tr8h_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5tr8l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5tr8l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (3 domains)

Domain ID domain_id	5tr8H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5tr8L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5tr8L02
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	98.463 Å
Unit-cell length b length_b	83.332 Å
Unit-cell length c length_c	83.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.69 °
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	2.010 Å
Low-resolution limit resolution_low	24.607 Å
R factor r_factor	0.1756
R_work r_work	0.1743
R_free r_free	0.1983

fit	/app/data/saxs_computation/tr/5tr8/5tr8.fit
pddf	/app/data/pr_computation/tr/5tr8/5tr8.pr.out
profile	/app/data/saxs_computation/tr/5tr8/5tr8.dat

Crystal structure of vaccine-elicited pan- influenza H1N1 neutralizing murine antibody 441D6.

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

441D6 Fab Light chain

State in the Current Structure

Other States of the Same Protein in the Database

441D6 Fab Heavy chain

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)