1yed

STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.4)

Method: X-RAY DIFFRACTION D_max: 117.2 Å Quality: GOOD

▼

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

IGG1 FAB FRAGMENT (D.2.4)

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 1–102	Not recorded	IGG1 FAB FRAGMENT (D.2.4) × 1 PNB 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 3.10 Å R-free 0.260
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–102	Not recorded	IGG1 FAB FRAGMENT (D.2.4) × 1 PNB 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 3.10 Å R-free 0.260

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 1YED	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AI1 HIV-1 V3 LOOP MIMIC Deposited 1996-11-06	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 1–100（100 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.80 Å
1CLO ANTI-CARCINOEMBRYONIC ANTIGEN MONOCLONAL ANTIBODY A5B7 Deposited 1996-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–101（101 aa） Fragment：ANTIGEN BINDING FRAGMENT, FAB	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1DBA THREE-DIMENSIONAL STRUCTURE OF AN ANTI-STEROID FAB' AND PROGESTERONE-FAB' COMPLEX Deposited 1992-11-10	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	EOH ETHANOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1DBB THREE-DIMENSIONAL STRUCTURE OF AN ANTI-STEROID FAB' AND PROGESTERONE-FAB' COMPLEX Deposited 1992-11-11	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	STR PROGESTERONE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
1DBJ MOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-ANTIGEN COMPLEMENTARITY Deposited 1993-08-24	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	AE2 AETIOCHOLANOLONE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
1DBK MOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-ANTIGEN COMPLEMENTARITY Deposited 1993-08-24	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	ANO 5-BETA-ANDROSTANE-3,17-DIONE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1DBM MOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-ANTIGEN COMPLEMENTARITY Deposited 1993-08-24	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	SIH PROGESTERONE-11-ALPHA-OL-HEMISUCCINATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
1FBI CRYSTAL STRUCTURE OF A CROSS-REACTION COMPLEX BETWEEN FAB F9.13.7 AND GUINEA-FOWL LYSOZYME Deposited 1995-01-19	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 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1FBI CRYSTAL STRUCTURE OF A CROSS-REACTION COMPLEX BETWEEN FAB F9.13.7 AND GUINEA-FOWL LYSOZYME Deposited 1995-01-19	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 Q 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1KEL CATALYTIC ANTIBODY 28B4 FAB FRAGMENT COMPLEXED WITH HAPTEN (1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO] METHYLPHOSPHONIC ACID) Deposited 1996-04-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa） Fragment：VARIABLE REGIONS OF LIGHT AND HEAVY CHAINS	Not recorded	AAH 1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO]METHYLPHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.90 Å R-free 0.258
1KEM CATALYTIC ANTIBODY 28B4 FAB FRAGMENT Deposited 1996-04-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa） Fragment：VARIABLE REGIONS OF LIGHT AND HEAVY CHAINS	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.20 Å R-free 0.288
1NTL Model of mouse Crry-Ig determined by solution scattering, curve fitting and homology modelling Deposited 2003-01-30	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 Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 98–324（227 aa） Fragment：Q64735 residues 83-401,P01868 residues 98-324 Chain B 98–324（227 aa） Fragment：Q64735 residues 83-401,P01868 residues 98-324	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution 30.00 Å
1OPG OPG2 FAB FRAGMENT Deposited 1995-04-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1T2Q The Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen Deposited 2004-04-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa）	Not recorded	GOL GLYCEROL × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG MME 5K, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.83 Å R-free 0.247
2ATY Complement receptor chimaeric conjugate CR2-Ig Deposited 2005-08-26	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 Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 98–324（227 aa） Chain B 98–324（227 aa）	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
2DBL MOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-ANTIGEN COMPLEMENTARITY Deposited 1994-02-08	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	S5H 5-ALPHA-PREGNANE-3-BETA-OL-HEMISUCCINATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
2DBL MOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-ANTIGEN COMPLEMENTARITY Deposited 1994-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain H 1–100（100 aa）	Not recorded	S5H 5-ALPHA-PREGNANE-3-BETA-OL-HEMISUCCINATE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å

15 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GC1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 125–226； UniProt 1–102 Author chain H； PDBConstruct 125–226； UniProt 1–102

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1yed
Deposition date deposition_date	1997-04-15
Structure title title	STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.4)
Keywords keywords	CATALYTIC ANTIBODY, TRANSITION STATE ANALOGUE; CATALYTIC ANTIBODY
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	35.38 Å
Radius of gyration Rg (electron density) rg_electron	34.97 Å
Forward intensity I(0) i0	150733000.00
Molecular weight molecular_weight	97828.0 kDa
Excluded volume excluded_volume	122170 Å³
Envelope volume envelope_volume	162730 Å³
Hydration-shell volume shell_volume	40972 Å³
Envelope diameter envelope_diameter	125.7 Å
Shell Rg shell_rg	39.29 Å
Envelope Rg envelope_rg	34.63 Å
Shape Rg shape_rg	34.94 Å
Total Rg total_rg	35.38 Å
Total atoms total_atoms	6882
Residues n_residues	858
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	117.2 Å
Rg (real space) rg_real	35.56 Å
Rg uncertainty (real space) rg_real_error	1.00 Å
I(0) (real space) i0_real	1.5070e+08
I(0) uncertainty (real space) i0_real_error	2.6010e+06
Rg (reciprocal space) rg_reciprocal	35.45 Å
I(0) (reciprocal space) i0_reciprocal	150700000.0000
Solution quality estimate total_estimate	0.8622
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.1 Å
Skewness Skewness skewness	0.493
Kurtosis Kurtosis kurtosis	-0.230
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15750000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.659

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	IGG1 FAB FRAGMENT (D.2.4)
Molecular weight formula_weight	24092.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,A
Atom count atom_count	6886

DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLESGVPDRFTGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 2 Entity 2 polymer

Description description	IGG1 FAB FRAGMENT (D.2.4)
Molecular weight formula_weight	24499.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,B

AVKLQQSGPELVRPGTSVKLSCKTSGYIFTSYWIHWLKQSSGQGLEWIARIYPGTGGTYYNEKFKGKATLTADKSSSTAYMQLSSLKSEDSAVYFCTRWGFTTVRENYYAMDYWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Entity 3 Entity 3 non-polymer

Description description	4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
Molecular weight formula_weight	360.3 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	4

▼

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1yeda1
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	d1yeda2
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	d1yedb1
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	d1yedb2
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	d1yedh1
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	d1yedh2
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	d1yedl1
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	d1yedl2
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 (8 domains)

Domain ID domain_id	1yedA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yedA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yedB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yedB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yedH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yedH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yedL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1yedL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	99.250 Å
Unit-cell length b length_b	104.790 Å
Unit-cell length c length_c	223.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2600

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

STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.4)

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

IGG1 FAB FRAGMENT (D.2.4)

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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)