SAXSdb — 1clz

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

IGG FAB (IGG3, KAPPA)

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	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–99	Fragment：FRAGMENT (MBR96)	IGG FAB (IGG3, KAPPA) × 1 alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NON METHYL NONANOATE (ESTER) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.8；pH 7.8	Resolution 2.80 Å R-free 0.295
2	Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–99	Fragment：FRAGMENT (MBR96)	IGG FAB (IGG3, KAPPA) × 1 alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NON METHYL NONANOATE (ESTER) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.8；pH 7.8	Resolution 2.80 Å R-free 0.295

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	GC3_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 120–218； 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	1clz
Deposition date deposition_date	1995-03-15
Structure title title	IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER
Keywords keywords	IMMUNOGLOBULIN C REGION, GLYCOPROTEIN, TRANSMEMBRANE, IMMUNOGLOBULIN; IMMUNOGLOBULIN
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	25.46 Å
Radius of gyration Rg (electron density) rg_electron	24.36 Å
Forward intensity I(0) i0	39867900.00
Molecular weight molecular_weight	48756.0 kDa
Excluded volume excluded_volume	60874 Å³
Envelope volume envelope_volume	73325 Å³
Hydration-shell volume shell_volume	25422 Å³
Envelope diameter envelope_diameter	87.9 Å
Shell Rg shell_rg	31.18 Å
Envelope Rg envelope_rg	24.18 Å
Shape Rg shape_rg	24.33 Å
Total Rg total_rg	25.20 Å
Total atoms total_atoms	3431
Residues n_residues	437
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	84.1 Å
Rg (real space) rg_real	25.46 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	3.9870e+07
I(0) uncertainty (real space) i0_real_error	5.1490e+05
Rg (reciprocal space) rg_reciprocal	25.46 Å
I(0) (reciprocal space) i0_reciprocal	39870000.0000
Solution quality estimate total_estimate	0.8956
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.328
Kurtosis Kurtosis kurtosis	-0.436
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8264000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.980

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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	IGG FAB (IGG3, KAPPA)
Molecular weight formula_weight	24246.9 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	3431

DVLMTQIPVSLPVSLGDQASISCRSSQIIVHNNGNTYLEWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 2 Entity 2 polymer

Description description	IGG FAB (IGG3, KAPPA)
Molecular weight formula_weight	23759.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVNLVESGGGLVQPGGSLKVSCVTSGFTFSDYYMYWVRQTPEKRLEWVAYISQGGDITDYPDTVKGRFTISRDNAKNSLYLQMSRLKSEDTAMYYCARGLDDGAWFAYWGQGTLVTVSVTTTAPSVYPLVPGCSDTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTVICNVAHPASKTELIKRIEPR

Entity 3 Entity 3 branched

Description description	alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	675.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	METHYL NONANOATE (ESTER)
Molecular weight formula_weight	172.3 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1clzh1
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	d1clzh2
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	d1clzl1
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	d1clzl2
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	1clzH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1clzH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1clzL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1clzL02
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 (2)

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Unit-cell length a length_a	69.400 Å
Unit-cell length b length_b	84.900 Å
Unit-cell length c length_c	86.800 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2950

fit	/app/data/saxs_computation/cl/1clz/1clz.fit
pddf	/app/data/pr_computation/cl/1clz/1clz.pr.out
profile	/app/data/saxs_computation/cl/1clz/1clz.dat

IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER

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

IGG FAB (IGG3, KAPPA)

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 branched

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)