SAXSdb — 1lo4

▼

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

If kappa light chain

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 L； UniProt 24–236	Fragment：Fab fragment	Ig gamma 2a heavy chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；290 K；PEG4000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.40 Å R-free 0.308

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 1LO4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1I9I NATIVE CRYSTAL STRUCTURE OF THE RECOMBINANT MONOCLONAL WILD TYPE ANTI-TESTOSTERONE FAB FRAGMENT Deposited 2001-03-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；peg3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.72 Å R-free 0.252
1I9J TESTOSTERONE COMPLEX STRUCTURE OF THE RECOMBINANT MONOCLONAL WILD TYPE ANTI-TESTOSTERONE FAB FRAGMENT Deposited 2001-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa）	Not recorded	TES TESTOSTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；peg3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.255
1L7T Crystal Structure Analysis of the anti-testosterone Fab fragment Deposited 2002-03-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa） Fragment：fab77 fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；peg3350, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.275
1LO2 Retro-Diels-Alderase Catalytic Antibody Deposited 2002-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 20–238（219 aa） Fragment：Fab fragment	Not recorded	OX1 [2'-CARBOXYLETHYL]-10-METHYL-ANTHRACENE ENDOPEROXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；290 K；PEG3350, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.248
1LO2 Retro-Diels-Alderase Catalytic Antibody Deposited 2002-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa） Fragment：Fab fragment	Not recorded	OX1 [2'-CARBOXYLETHYL]-10-METHYL-ANTHRACENE ENDOPEROXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；290 K；PEG3350, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.248
1LO3 Retro-Diels-Alderase Catalytic Antibody: Product Analogue Deposited 2002-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 20–238（219 aa） Fragment：Fab fragment	Not recorded	AN1 3-(10-METHYL-ANTHRACEN-9-YL)-PROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；PEG3350, pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.259
1LO3 Retro-Diels-Alderase Catalytic Antibody: Product Analogue Deposited 2002-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–238（219 aa） Fragment：Fab fragment	Not recorded	AN1 3-(10-METHYL-ANTHRACEN-9-YL)-PROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；PEG3350, pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.259
1N4X Structure of scFv 1696 at acidic pH Deposited 2002-11-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 23–130（108 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.256
1N4X Structure of scFv 1696 at acidic pH Deposited 2002-11-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 23–130（108 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.256

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q99M37
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 5–217； UniProt 24–236

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1lo4
Deposition date deposition_date	2002-05-06
Structure title title	Retro-Diels-Alderase Catalytic antibody 9D9
Keywords keywords	Fab, catalytic antibody, retro-Deils-Alderase, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	25.19 Å
Radius of gyration Rg (electron density) rg_electron	24.16 Å
Forward intensity I(0) i0	38496100.00
Molecular weight molecular_weight	47610.0 kDa
Excluded volume excluded_volume	59384 Å³
Envelope volume envelope_volume	72503 Å³
Hydration-shell volume shell_volume	25102 Å³
Envelope diameter envelope_diameter	81.9 Å
Shell Rg shell_rg	31.25 Å
Envelope Rg envelope_rg	23.99 Å
Shape Rg shape_rg	24.14 Å
Total Rg total_rg	25.03 Å
Total atoms total_atoms	3352
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

▼

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

Maximum dimension Dmax dmax	79.3 Å
Rg (real space) rg_real	25.16 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	3.8500e+07
I(0) uncertainty (real space) i0_real_error	5.6550e+05
Rg (reciprocal space) rg_reciprocal	25.17 Å
I(0) (reciprocal space) i0_reciprocal	38500000.0000
Solution quality estimate total_estimate	0.9099
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.0 Å
Skewness Skewness skewness	0.268
Kurtosis Kurtosis kurtosis	-0.515
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8046000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.986

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	If kappa light chain
Molecular weight formula_weight	23994.5 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	3371

DVLLTQTPLSLPVSLGDQASISCRSSQTIVHTNGNTYFEWYLQKPGQSPHLLIYKVSNRLSGVPDRFSGSGSGTDFTLKISRVEAEDLGLYYCFQGSHSPWTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Entity 2 Entity 2 polymer

Description description	Ig gamma 2a heavy chain
Molecular weight formula_weight	23656.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

ELKLVETGGDLVKPGGSLTLSCEASGFTLRTYGMSWVRQTPQMRLEWVASISYGGLLYFSDSVKGRFTISRDIVRNILTLQMSRLRSEDTAIYYCARGTSFVRYFDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTQVDKKIVPRAA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1lo4h1
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	d1lo4h2
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	d1lo4l1
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	d1lo4l2
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	1lo4H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1lo4H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1lo4L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1lo4L02
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	48.703 Å
Unit-cell length b length_b	80.355 Å
Unit-cell length c length_c	125.103 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	2.400 Å
Low-resolution limit resolution_low	38.350 Å
R factor r_factor	0.2392
R_work r_work	0.2353
R_free r_free	0.3079

fit	/app/data/saxs_computation/lo/1lo4/1lo4.fit
pddf	/app/data/pr_computation/lo/1lo4/1lo4.pr.out
profile	/app/data/saxs_computation/lo/1lo4/1lo4.dat

Retro-Diels-Alderase Catalytic antibody 9D9

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 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)