1loa

THREE-DIMENSIONAL STRUCTURES OF COMPLEXES OF LATHYRUS OCHRUS ISOLECTIN I WITH GLUCOSE AND MANNOSE: FINE SPECIFICITY OF THE MONOSACCHARIDE-BINDING SITE

Method: X-RAY DIFFRACTION Dmax: 100.2 Å Quality: REASONABLE

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

LEGUME ISOLECTIN I (ALPHA CHAIN)

Lathyrus ochrus

UniProt P04122

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–181 Chain C; UniProt 1–181 Not recorded LEGUME ISOLECTIN I (BETA CHAIN) × 2 (P12306) GYP methyl alpha-D-glucopyranoside × 2 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.20 Å
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 1–181 Chain G; UniProt 1–181 Not recorded LEGUME ISOLECTIN I (BETA CHAIN) × 2 (P12306) GYP methyl alpha-D-glucopyranoside × 2 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.20 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.

8 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LECB_LATOC
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–181; UniProt 1–181 Author chain C; PDBConstruct 1–181; UniProt 1–181 Author chain E; PDBConstruct 1–181; UniProt 1–181 Author chain G; PDBConstruct 1–181; UniProt 1–181

LEGUME ISOLECTIN I (BETA CHAIN)

Lathyrus ochrus

UniProt P12306

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–52 Chain D; UniProt 1–52 Not recorded LEGUME ISOLECTIN I (ALPHA CHAIN) × 2 (P04122) GYP methyl alpha-D-glucopyranoside × 2 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.20 Å
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 1–52 Chain H; UniProt 1–52 Not recorded LEGUME ISOLECTIN I (ALPHA CHAIN) × 2 (P04122) GYP methyl alpha-D-glucopyranoside × 2 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.20 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.

6 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LEC1_LATOC
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–52; UniProt 1–52 Author chain D; PDBConstruct 1–52; UniProt 1–52 Author chain F; PDBConstruct 1–52; UniProt 1–52 Author chain H; PDBConstruct 1–52; UniProt 1–52

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1loa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1loa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1loa
Deposition date deposition_date1993-01-27
Structure title titleTHREE-DIMENSIONAL STRUCTURES OF COMPLEXES OF LATHYRUS OCHRUS ISOLECTIN I WITH GLUCOSE AND MANNOSE: FINE SPECIFICITY OF THE MONOSACCHARIDE-BINDING SITE
Keywords keywordsLECTIN; LECTIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.76
Radius of gyration Rg (electron density) rg_electron31.62
Forward intensity I(0) i0155042000.00
Molecular weight molecular_weight101160.0 kDa
Excluded volume excluded_volume127000 ų
Envelope volume envelope_volume153080 ų
Hydration-shell volume shell_volume40498 ų
Envelope diameter envelope_diameter103.9
Shell Rg shell_rg38.50
Envelope Rg envelope_rg31.24
Shape Rg shape_rg31.59
Total Rg total_rg32.29
Total atoms total_atoms7162
Residues n_residues908
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax100.2
Rg (real space) rg_real32.57
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real1.5500e+08
I(0) uncertainty (real space) i0_real_error2.2220e+06
Rg (reciprocal space) rg_reciprocal32.66
I(0) (reciprocal space) i0_reciprocal155100000.0000
Solution quality estimate total_estimate0.7126
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.0
Skewness Skewness skewness0.061
Kurtosis Kurtosis kurtosis-0.683
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30170000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 1.000; Smooth: 0.954

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1loa.1
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.1 — Legume lectins
Domain ID domain_idd1loa.2
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.1 — Legume lectins
Domain ID domain_idd1loa.3
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.1 — Legume lectins
Domain ID domain_idd1loa.4
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.1 — Legume lectins

CATH v4.4 (4 domains)

Domain ID domain_id1loaA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id1loaC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id1loaE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id1loaG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200

8. Citations (2)

9. Files and Curves (10)