SAXSdb — 5t7p

▼

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

Lectin

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 31–266 Chain B； UniProt 31–266	Fragment：UNP residues 31-266	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2 XMM 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；100 mM HEPES pH 6.8, 20% PEG 8000, 200 mM Magnesium acetate tetrahydrate	Resolution 2.16 Å R-free 0.221

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 5T7P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BQP THE STRUCTURE OF THE PEA LECTIN-D-MANNOPYRANOSE COMPLEX Deposited 1998-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–211（181 aa） Fragment：BETA CHAIN Chain B 218–264（47 aa） Fragment：ALPHA CHAIN	Not recorded	CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 MAN alpha-D-mannopyranose × 1 BMA beta-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.10 Å R-free 0.188
1BQP THE STRUCTURE OF THE PEA LECTIN-D-MANNOPYRANOSE COMPLEX Deposited 1998-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 31–211（181 aa） Fragment：BETA CHAIN Chain D 218–264（47 aa） Fragment：ALPHA CHAIN	Not recorded	CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 MAN alpha-D-mannopyranose × 1 BMA beta-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.10 Å R-free 0.188
1BQP THE STRUCTURE OF THE PEA LECTIN-D-MANNOPYRANOSE COMPLEX Deposited 1998-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–211（181 aa） Fragment：BETA CHAIN Chain B 218–264（47 aa） Fragment：ALPHA CHAIN Chain C 31–211（181 aa） Fragment：BETA CHAIN Chain D 218–264（47 aa） Fragment：ALPHA CHAIN	Not recorded	CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 MAN alpha-D-mannopyranose × 2 BMA beta-D-mannopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.10 Å R-free 0.188
1HKD Structure of pea lectin in complex with alpha-methyl-D-glucopyranoside Deposited 2003-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–211（181 aa） Fragment：RESIDUES 31-211 Chain B 218–269（52 aa） Fragment：RESIDUES 218-269 Chain C 31–211（181 aa） Fragment：RESIDUES 31-211 Chain D 218–269（52 aa） Fragment：RESIDUES 218-269	Not recorded	CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 GYP methyl alpha-D-glucopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；1.7 M AMMONIUM SULFATE, 10% (V/V) ETHANOL, pH 7.00	Resolution 2.09 Å R-free 0.209
1OFS Pea lectin-sucrose complex Deposited 2003-04-19	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 31–217（187 aa） Fragment：RESIDUES 31-217 Chain B 218–265（48 aa） Fragment：RESIDUES 218-265 Chain C 31–217（187 aa） Fragment：RESIDUES 31-217 Chain D 218–265（48 aa） Fragment：RESIDUES 218-265	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M MES PH 6.5, 12% (W/V) PEG 20K, 8% (V/V) ETOH, 40 MM SUCROSE; CRYOSOLUTION: 0.1 M MES PH 6.5, 17% PEG 20K, 60% (V/V) ETOH, 25 MM SUCROSE	Resolution 1.80 Å R-free 0.207
1RIN X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION Deposited 1993-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–210（180 aa） Chain B 218–266（49 aa） Chain C 31–210（180 aa） Chain D 218–266（49 aa）	Not recorded	MAN alpha-D-mannopyranose × 2 MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1RIN X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION Deposited 1993-01-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–210（180 aa） Chain B 218–266（49 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1RIN X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION Deposited 1993-01-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 31–210（180 aa） Chain D 218–266（49 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
2BQP THE STRUCTURE OF THE PEA LECTIN-D-GLUCOPYRANOSE COMPLEX Deposited 1998-12-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–264（234 aa） Chain B 31–264（234 aa）	Not recorded	GLC alpha-D-glucopyranose × 2 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.90 Å R-free 0.188
2LTN DESIGN, EXPRESSION, AND CRYSTALLIZATION OF RECOMBINANT LECTIN FROM THE GARDEN PEA (PISUM SATIVUM) Deposited 1990-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 31–211（181 aa） Chain B 218–269（52 aa） Chain C 31–211（181 aa） Chain D 218–269（52 aa）	Not recorded	MN MANGANESE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
2LTN DESIGN, EXPRESSION, AND CRYSTALLIZATION OF RECOMBINANT LECTIN FROM THE GARDEN PEA (PISUM SATIVUM) Deposited 1990-06-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 31–211（181 aa） Chain D 218–269（52 aa）	Not recorded	MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
2LTN DESIGN, EXPRESSION, AND CRYSTALLIZATION OF RECOMBINANT LECTIN FROM THE GARDEN PEA (PISUM SATIVUM) Deposited 1990-06-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–211（181 aa） Chain B 218–269（52 aa）	Not recorded	MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LEC_PEA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–236； UniProt 31–266 Author chain B； PDBConstruct 1–236； UniProt 31–266

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	5t7p
Deposition date deposition_date	2016-09-05
Structure title title	Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man
Keywords keywords	Pisum arvense, lectin, PAL, X-Man., SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	26.08 Å
Radius of gyration Rg (electron density) rg_electron	25.42 Å
Forward intensity I(0) i0	42905700.00
Molecular weight molecular_weight	51184.0 kDa
Excluded volume excluded_volume	63981 Å³
Envelope volume envelope_volume	74238 Å³
Hydration-shell volume shell_volume	25320 Å³
Envelope diameter envelope_diameter	89.2 Å
Shell Rg shell_rg	31.69 Å
Envelope Rg envelope_rg	25.46 Å
Shape Rg shape_rg	25.39 Å
Total Rg total_rg	26.22 Å
Total atoms total_atoms	3610
Residues n_residues	456
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	85.4 Å
Rg (real space) rg_real	26.18 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	4.2910e+07
I(0) uncertainty (real space) i0_real_error	6.5340e+05
Rg (reciprocal space) rg_reciprocal	26.15 Å
I(0) (reciprocal space) i0_reciprocal	42900000.0000
Solution quality estimate total_estimate	0.8803
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.431
Kurtosis Kurtosis kurtosis	-0.447
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8698000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.969

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Lectin
Molecular weight formula_weight	26019.6 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3921

TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYPNSLEEENVTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELSGT

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
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	5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside
Molecular weight formula_weight	408.6 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	311

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5t7pa_
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	d5t7pb_
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	5t7pA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	5t7pB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	56.770 Å
Unit-cell length b length_b	62.970 Å
Unit-cell length c length_c	66.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.160 Å
Low-resolution limit resolution_low	33.277 Å
R factor r_factor	0.1729
R_work r_work	0.1704
R_free r_free	0.2208

fit	/app/data/saxs_computation/t7/5t7p/5t7p.fit
pddf	/app/data/pr_computation/t7/5t7p/5t7p.pr.out
profile	/app/data/saxs_computation/t7/5t7p/5t7p.dat

Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man

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