SAXSdb — 1rin

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

PEA LECTIN

Pisum sativum

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 31–210 Chain B； UniProt 218–266 Chain C； UniProt 31–210 Chain D； UniProt 218–266	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 experimental conditions	Resolution 2.60 Å
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 31–210 Chain B； UniProt 218–266	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 experimental conditions	Resolution 2.60 Å
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 31–210 Chain D； UniProt 218–266	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 experimental conditions	Resolution 2.60 Å

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 1RIN	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 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 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 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
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 ligand/ion 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 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 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
5T7P Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man Deposited 2016-09-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–266（236 aa） Fragment：UNP residues 31-266 Chain B 31–266（236 aa） Fragment：UNP residues 31-266	Not recorded	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

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LEC_PEA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–180； UniProt 31–210 Author chain C； PDBConstruct 1–180； UniProt 31–210 Author chain B； PDBConstruct 1–49； UniProt 218–266 Author chain D； PDBConstruct 1–49； UniProt 218–266

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1rin
Deposition date deposition_date	1993-01-27
Structure title title	X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION
Keywords keywords	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	25.82 Å
Radius of gyration Rg (electron density) rg_electron	24.87 Å
Forward intensity I(0) i0	41868300.00
Molecular weight molecular_weight	50782.0 kDa
Excluded volume excluded_volume	63662 Å³
Envelope volume envelope_volume	73094 Å³
Hydration-shell volume shell_volume	25277 Å³
Envelope diameter envelope_diameter	89.0 Å
Shell Rg shell_rg	31.21 Å
Envelope Rg envelope_rg	25.05 Å
Shape Rg shape_rg	24.83 Å
Total Rg total_rg	25.71 Å
Total atoms total_atoms	3591
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

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

Maximum dimension Dmax dmax	86.5 Å
Rg (real space) rg_real	25.94 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	4.1870e+07
I(0) uncertainty (real space) i0_real_error	5.7750e+05
Rg (reciprocal space) rg_reciprocal	25.90 Å
I(0) (reciprocal space) i0_reciprocal	41870000.0000
Solution quality estimate total_estimate	0.8696
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.466
Kurtosis Kurtosis kurtosis	-0.356
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7383000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PEA LECTIN
Molecular weight formula_weight	19888.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3678

TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTETVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYP

来源 Source

来源生物 organism	Pisum sativum
通用名 common_name	pea
NCBI Class编号 ncbi_taxonomy_id	3888

Entity 2 Entity 2 polymer

Description description	PEA LECTIN
Molecular weight formula_weight	5334.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELSGT

来源 Source

来源生物 organism	Pisum sativum
通用名 common_name	pea
NCBI Class编号 ncbi_taxonomy_id	3888

Entity 3 Entity 3 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
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

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1rin.1
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	d1rin.2
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	1rinA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1rinC00
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 (2)

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Unit-cell length a length_a	64.300 Å
Unit-cell length b length_b	73.400 Å
Unit-cell length c length_c	108.500 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	8

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	—

fit	/app/data/saxs_computation/ri/1rin/1rin.fit
pddf	/app/data/pr_computation/ri/1rin/1rin.pr.out
profile	/app/data/saxs_computation/ri/1rin/1rin.dat

X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION

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

PEA 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

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)