SAXSdb — 1lu2

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

LECTIN

Vigna unguiculata subsp. cylindrica

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 23–275 Chain B； UniProt 23–275	Not recorded	A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 4 CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.6；100 MM NACACO PH 6.6 15% (W/V) PEG-ME 5000 10 MM BLOOD GROUP A TRISACCHARIDE	Resolution 2.80 Å R-free 0.219

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 1LU2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BJQ THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH ADENINE Deposited 1998-06-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–275（253 aa） Chain B 23–275（253 aa） Chain C 23–275（253 aa） Chain D 23–275（253 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 ADE ADENINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；100 MM NA-CACODYLATE PH 6.5 10 % (W/V) PEG 8000 20 MM MGAC2 1 MM ADENINE	Resolution 2.65 Å R-free 0.246
1BJQ THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH ADENINE Deposited 1998-06-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 23–275（253 aa） Chain F 23–275（253 aa） Chain G 23–275（253 aa） Chain H 23–275（253 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 ADE ADENINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；100 MM NA-CACODYLATE PH 6.5 10 % (W/V) PEG 8000 20 MM MGAC2 1 MM ADENINE	Resolution 2.65 Å R-free 0.246
1LU1 THE STRUCTURE OF THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE FORSSMAN DISACCHARIDE Deposited 1998-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–275（253 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 ADE ADENINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；100 MM HEPES PH 7.5 0.2 M MGCL2 30% (W/V) PEG 400	Resolution 2.60 Å R-free 0.234

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LEC1_DOLBI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–253； UniProt 23–275 Author chain B； PDBConstruct 1–253； UniProt 23–275

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	1lu2
Deposition date deposition_date	1998-07-30
Structure title title	DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE BLOOD GROUP A TRISACCHARIDE
Keywords keywords	LEGUME LECTINS, DOLICHOS BIFLORUS SEED LECTIN, SUGAR BINDING, LECTIN; LECTIN
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	24.89 Å
Forward intensity I(0) i0	47083800.00
Molecular weight molecular_weight	53659.0 kDa
Excluded volume excluded_volume	67175 Å³
Envelope volume envelope_volume	78682 Å³
Hydration-shell volume shell_volume	26957 Å³
Envelope diameter envelope_diameter	86.8 Å
Shell Rg shell_rg	31.78 Å
Envelope Rg envelope_rg	24.94 Å
Shape Rg shape_rg	24.83 Å
Total Rg total_rg	25.85 Å
Total atoms total_atoms	3788
Residues n_residues	506
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	83.0 Å
Rg (real space) rg_real	26.03 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	4.7080e+07
I(0) uncertainty (real space) i0_real_error	7.2660e+05
Rg (reciprocal space) rg_reciprocal	26.01 Å
I(0) (reciprocal space) i0_reciprocal	47080000.0000
Solution quality estimate total_estimate	0.8943
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.2 Å
Skewness Skewness skewness	0.395
Kurtosis Kurtosis kurtosis	-0.421
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7811000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.930

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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	LECTIN
Molecular weight formula_weight	27115.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3788

ANIQSFSFKNFNSPSFILQGDATVSSGKLQLTKVKENGIPTPSSLGRAFYSSPIQIYDKSTGAVASWATSFTVKISAPSKASFADGIAFALVPVGSEPRRNGGYLGVFDSDVYNNSAQTVAVEFDTLSNSGWDPSMKHIGIDVNSIKSIATVSWDLANGENAEILITYNAATSLLVASLVHPSRRTSYILSERVDITNELPEYVSVGFSATTGLSEGYIETHDVLSWSFASKLPDDSTAEPLDLASYLVRNVL

来源 Source

来源生物 organism	Vigna unguiculata subsp. cylindrica
通用名 common_name	horse gram
NCBI Class编号 ncbi_taxonomy_id	3840
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-alpha-D-galactopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1lu2a_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.1 — Legume lectins

Domain ID domain_id	d1lu2b_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.1 — Legume lectins

CATH v4.4 (2 domains)

Domain ID domain_id	1lu2A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1lu2B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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8. Citations (1)

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Unit-cell length a length_a	96.730 Å
Unit-cell length b length_b	108.000 Å
Unit-cell length c length_c	80.960 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	124.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1910
R_work r_work	0.1910
R_free r_free	0.2190

fit	/app/data/saxs_computation/lu/1lu2/1lu2.fit
pddf	/app/data/pr_computation/lu/1lu2/1lu2.pr.out
profile	/app/data/saxs_computation/lu/1lu2/1lu2.dat

DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH THE BLOOD GROUP A TRISACCHARIDE

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

LECTIN

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