SAXSdb — 3eyu

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

If kappa 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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain L； UniProt 1–219	Non-standard monomer：Yes (specific site not provided by mmCIF)	PFA1 Fab Heavy Chain × 1 ROR2(518-525) peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；20% w/v PEG3350, 0.2 M LiCl, vapor diffusion, sitting drop, temperature 298K	Resolution 2.71 Å R-free 0.248

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 3EYU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZEA Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide Deposited 2005-04-18	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 L 1–216（216 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；PEG 8000, citrat buffer, potassium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.78 Å R-free 0.248
2DTM Thermodynamic and structural analyses of hydrolytic mechanism by catalytic antibodies Deposited 2006-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–219（219 aa） Fragment：FAB FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；50mM Tris-HCl(pH 8.7), 16%(w/v) PEG4000, 0.1mM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.25 Å R-free 0.278
2IPT PFA1 Fab Fragment Deposited 2006-10-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–219（219 aa）	Not recorded	ACM ACETAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；294 K；0.1 M Hepes, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 294K	Resolution 2.00 Å R-free 0.223
2IQA PFA2 FAB fragment, monoclinic apo form Deposited 2006-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–219（219 aa）	Not recorded	ACM ACETAMIDE × 1 GOL GLYCEROL × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；0.1 M Bis-Tris, 28% PEG-MME 2000, pH 6.5, VAPOR DIFFUSION	Resolution 2.00 Å R-free 0.279
2IQA PFA2 FAB fragment, monoclinic apo form Deposited 2006-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–219（219 aa）	Not recorded	ACM ACETAMIDE × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；0.1 M Bis-Tris, 28% PEG-MME 2000, pH 6.5, VAPOR DIFFUSION	Resolution 2.00 Å R-free 0.279
2R0W PFA2 FAB complexed with Abeta1-8 Deposited 2007-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–219（219 aa） Fragment：light chain	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.3；295 K；25% PEG-MME 5000, 0.1 M OAc, pH 5.3, VAPOR DIFFUSION, temperature 295K	Resolution 2.50 Å R-free 0.277
2R0Z PFA1 FAB complexed with GripI peptide fragment Deposited 2007-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–219（219 aa） Fragment：light chain	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；295 K；PEG, VAPOR DIFFUSION, temperature 295K	Resolution 2.10 Å R-free 0.261
3EYS PFA1 Fab fragment complexed with pyro-Glu3-A-Beta (3-8) Deposited 2008-10-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–219（219 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；25% w/v PEG2000-MME, pH 8.5, vapor diffusion, sitting drop, temperature 298K	Resolution 1.95 Å R-free 0.256
4P3D MT1-MMP:Fab complex (Form II) Deposited 2014-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–217（217 aa） Chain L 1–217（217 aa）	Not recorded	CL CHLORIDE ION × 2 GOL GLYCEROL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 EDO 1,2-ETHANEDIOL × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% PEG 3350, 0.2M MgCl.hexahydrate, 0.1M Hepes	Resolution 1.95 Å R-free 0.210
4TPR Structure of Tau5 antibody Fab fragment Deposited 2014-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: Dimeric	Chain L 1–218（218 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 CL CHLORIDE ION × 5 PGE TRIETHYLENE GLYCOL × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 5 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 33O 3,6,9,12,15,18,21,24,27,30,33,36-dodecaoxaoctatriacontane-1,38-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.2 M NaCl, 0.1 M Bis-Tris, 25 % w/v PEG 3350	Resolution 1.60 Å R-free 0.191
4TQE Structure of tau peptide in complex with Tau5 antibody Fab fragment Deposited 2014-06-11	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 L 1–218（218 aa）	Not recorded	SO4 SULFATE ION × 5 NA SODIUM ION × 4 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M lithium sulphate, 30% PEG 4000, 0.1M Tris pH 8.5	Resolution 1.60 Å R-free 0.197
6PXR Anti-TAU BIIB092 FAB with TAU peptide Deposited 2019-07-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 103–219（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Tris-HCl, pH 8.5, 20% w/v PEG2000 MME, 200 mM trimethylamine N-oxide, 100 mM non-detergent sulfobetaine 201	Resolution 1.56 Å R-free 0.268
7A6C Nanodisc reconstituted human ABCB1 in complex with MRK16 Fab and elacridar Deposited 2020-08-25	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–219（219 aa）	Not recorded	R0Z elacridar × 2 CLR CHOLESTEROL × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A2NHM3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–219； UniProt 1–219

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	3eyu
Deposition date deposition_date	2008-10-21
Structure title title	PFA1 Fab fragment complexed with Ror2(518-525)
Keywords keywords	;Fab, amyloid, alzheimer's, protein-peptide complex, 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	26.33 Å
Radius of gyration Rg (electron density) rg_electron	25.19 Å
Forward intensity I(0) i0	39410500.00
Molecular weight molecular_weight	48229.0 kDa
Excluded volume excluded_volume	60175 Å³
Envelope volume envelope_volume	74579 Å³
Hydration-shell volume shell_volume	25076 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	32.05 Å
Envelope Rg envelope_rg	24.81 Å
Shape Rg shape_rg	25.17 Å
Total Rg total_rg	26.03 Å
Total atoms total_atoms	3398
Residues n_residues	442
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	82.9 Å
Rg (real space) rg_real	26.33 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	3.9410e+07
I(0) uncertainty (real space) i0_real_error	5.9940e+05
Rg (reciprocal space) rg_reciprocal	26.33 Å
I(0) (reciprocal space) i0_reciprocal	39410000.0000
Solution quality estimate total_estimate	0.9085
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.273
Kurtosis Kurtosis kurtosis	-0.593
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6019000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.966

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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	If kappa light chain
Molecular weight formula_weight	24203.9 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	3421

DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

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	Mus musculus

Entity 2 Entity 2 polymer

Description description	PFA1 Fab Heavy Chain
Molecular weight formula_weight	24210.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVTLKESGPGILKPSQTLSLTCSFSGFSLSTSGMGVGWIRQPSGKGLEWLAHIWWDDDRSYNPSLKSQLTISKDAARNQVFLRITSVDTADTATYYCVRRAHTTVLGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT

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	Mus musculus

Entity 3 Entity 3 polymer

Description description	ROR2(518-525) peptide
Molecular weight formula_weight	1076.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

REEFRHEA

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3eyuH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3eyuH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3eyuL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3eyuL02
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	41.632 Å
Unit-cell length b length_b	42.632 Å
Unit-cell length c length_c	58.729 Å
Unit-cell angle α angle_alpha	96.09 °
Unit-cell angle β angle_beta	93.58 °
Unit-cell angle γ angle_gamma	91.71 °
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	—

Resolution resolution	2.710 Å
Low-resolution limit resolution_low	21.290 Å
R factor r_factor	0.1800
R_work r_work	0.1770
R_free r_free	0.2480

fit	/app/data/saxs_computation/ey/3eyu/3eyu.fit
pddf	/app/data/pr_computation/ey/3eyu/3eyu.pr.out
profile	/app/data/saxs_computation/ey/3eyu/3eyu.dat

PFA1 Fab fragment complexed with Ror2(518-525)

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

If kappa light 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 polymer

Polymer Polymer

Entity 4 Entity 4 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)