SAXSdb — 1yec

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

IGG2A FAB FRAGMENT (D2.3)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–99	Not recorded	IGG2A FAB FRAGMENT (D2.3) × 1 ZN ZINC ION × 7 PNB 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 1.90 Å R-free 0.252
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–99	Not recorded	IGG2A FAB FRAGMENT (D2.3) × 1 ZN ZINC ION × 7 PNB 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 1.90 Å R-free 0.252

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 1YEC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GGI CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN Deposited 1993-04-02	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 H 1–107（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1GGI CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN Deposited 1993-04-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–107（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1IGT STRUCTURE OF IMMUNOGLOBULIN Deposited 1996-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–326（326 aa） Chain D 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；291 K；7 MICROLITERS OF 4.3 MG/ML MAB231, 3 MICROLITERS 50 MILLIMOLAR TRIS PH 8.0, AND 7 MICROLITERS 4% PEG 3350 EQUILIBRATED AGAINST 25 ML RESERVOIRS OF 4% PEG 3350, AT 18 DEGREE CELSIUS (SANDWICH PLATE)., temperature 291K	Resolution 2.80 Å R-free 0.297
1YEF STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE ANALOGUE Deposited 1997-05-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 8 PNC PARA-NITROBENZYL GLUTARYL GLYCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.248
1YEG STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT Deposited 1997-05-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 BPN PARANITROBENZYL ALCOHOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.240
1YEG STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT Deposited 1997-05-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 BPN PARANITROBENZYL ALCOHOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.240
1YEH STRUCTURE OF IGG2A FAB FRAGMENT Deposited 1997-05-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 35% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.55 Å R-free 0.231
1YEH STRUCTURE OF IGG2A FAB FRAGMENT Deposited 1997-05-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 35% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.55 Å R-free 0.231
3OZ9 Crystal Structure of anti-gp41 Fab NC-1 Deposited 2010-09-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–100（100 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.13M sodium citrate, 0.1M sodium borate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.233
3ZO0 Mouse IgG2a in complex with mouse TRIM21 PRYSPRY Deposited 2013-02-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 120–327（208 aa） Fragment：FC, RESIDUES 120-327	Not recorded	MAN alpha-D-mannopyranose × 2 FUC alpha-L-fucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.99 Å R-free 0.253
5VAA Crystal structure of mouse IgG2a Fc T370K mutant Deposited 2017-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 107–330（224 aa） Fragment：UNP residues 107-330 Chain B 107–330（224 aa） Fragment：UNP residues 107-330	Mutation：T370K Mutation：T370K	GOL GLYCEROL × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；40% (w/v) PEG 200, 0.1 M MES, pH 6.5	Resolution 1.55 Å R-free 0.195
8AQW BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 98–330（233 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9RBQ Semliki Forest virus trimer 1 in complex with ApoER2 LA5 Deposited 2025-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: 13-meric	Chain A 99–330（232 aa）	Not recorded	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

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

View Construct and Data Evidence

UniProt name	GCAA_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 124–222； UniProt 1–99

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	1yec
Deposition date deposition_date	1997-04-15
Structure title title	STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3)
Keywords keywords	CATALYTIC ANTIBODY, TRANSITION STATE ANALOGUE; CATALYTIC ANTIBODY
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	25.98 Å
Radius of gyration Rg (electron density) rg_electron	24.85 Å
Forward intensity I(0) i0	41278900.00
Molecular weight molecular_weight	48971.0 kDa
Excluded volume excluded_volume	60783 Å³
Envelope volume envelope_volume	74476 Å³
Hydration-shell volume shell_volume	25242 Å³
Envelope diameter envelope_diameter	87.8 Å
Shell Rg shell_rg	31.81 Å
Envelope Rg envelope_rg	24.52 Å
Shape Rg shape_rg	24.74 Å
Total Rg total_rg	25.95 Å
Total atoms total_atoms	3419
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	86.0 Å
Rg (real space) rg_real	25.98 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	4.1280e+07
I(0) uncertainty (real space) i0_real_error	6.3390e+05
Rg (reciprocal space) rg_reciprocal	25.98 Å
I(0) (reciprocal space) i0_reciprocal	41280000.0000
Solution quality estimate total_estimate	0.8967
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.299
Kurtosis Kurtosis kurtosis	-0.491
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7922000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.977

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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	IGG2A FAB FRAGMENT (D2.3)
Molecular weight formula_weight	24005.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3568

DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIHLVSKLDSGVPDRITGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRGDAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 2 Entity 2 polymer

Description description	IGG2A FAB FRAGMENT (D2.3)
Molecular weight formula_weight	24189.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EMQLQQSGAELLRPGTSVKLSCKTSGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYYNEKFKGKATLTADKSSSTAYMQLSTLKSEDSAVYFCTRWGFIPVREDYVMDYWGQGTLVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP

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	7

Entity 4 Entity 4 non-polymer

Description description	4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
Molecular weight formula_weight	360.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	149

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yech1
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	d1yech2
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)

Domain ID domain_id	d1yecl1
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	d1yecl2
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 (4 domains)

Domain ID domain_id	1yecH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yecH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yecL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yecL02
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	78.180 Å
Unit-cell length b length_b	78.180 Å
Unit-cell length c length_c	158.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2520

fit	/app/data/saxs_computation/ye/1yec/1yec.fit
pddf	/app/data/pr_computation/ye/1yec/1yec.pr.out
profile	/app/data/saxs_computation/ye/1yec/1yec.dat

STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3)

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

IGG2A FAB FRAGMENT (D2.3)

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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)