1log

X-RAY STRUCTURE OF A (ALPHA-MAN(1-3)BETA-MAN(1-4)GLCNAC)-LECTIN COMPLEX AT 2.1 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 88.4 Å Quality: GOOD

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

LEGUME ISOLECTIN I (ALPHA CHAIN)

OrganismNot specified

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 Other combination Heteromer Protein × 4 其他Polymer 2 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) alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.10 Å
2 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–181 Not recorded LEGUME ISOLECTIN I (BETA CHAIN) × 1 (P12306) alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.10 Å
3 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–181 Not recorded LEGUME ISOLECTIN I (BETA CHAIN) × 1 (P12306) alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.10 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 26 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

LEGUME ISOLECTIN I (BETA CHAIN)

OrganismNot specified

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 Other combination Heteromer Protein × 4 其他Polymer 2 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) alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.10 Å
2 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–52 Not recorded LEGUME ISOLECTIN I (ALPHA CHAIN) × 1 (P04122) alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.10 Å
3 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–52 Not recorded LEGUME ISOLECTIN I (ALPHA CHAIN) × 1 (P04122) alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.10 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 22 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

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 1log

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1log
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1log
Deposition date deposition_date1994-01-27
Structure title titleX-RAY STRUCTURE OF A (ALPHA-MAN(1-3)BETA-MAN(1-4)GLCNAC)-LECTIN COMPLEX AT 2.1 ANGSTROMS RESOLUTION
Keywords keywordsLECTIN; LECTIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.09
Radius of gyration Rg (electron density) rg_electron25.16
Forward intensity I(0) i043000700.00
Molecular weight molecular_weight51663.0 kDa
Excluded volume excluded_volume64757 ų
Envelope volume envelope_volume74215 ų
Hydration-shell volume shell_volume25399 ų
Envelope diameter envelope_diameter91.6
Shell Rg shell_rg31.51
Envelope Rg envelope_rg25.42
Shape Rg shape_rg25.11
Total Rg total_rg26.02
Total atoms total_atoms3655
Residues n_residues458
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 dmax88.4
Rg (real space) rg_real26.23
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real4.3000e+07
I(0) uncertainty (real space) i0_real_error6.4880e+05
Rg (reciprocal space) rg_reciprocal26.19
I(0) (reciprocal space) i0_reciprocal43000000.0000
Solution quality estimate total_estimate0.8622
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.1
Skewness Skewness skewness0.477
Kurtosis Kurtosis kurtosis-0.364
Angular range angular_range— – 0.3050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7225000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.882; Smooth: 0.973

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1log.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_idd1log.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

CATH v4.4 (2 domains)

Domain ID domain_id1logA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id1logC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200

8. Citations (2)

9. Files and Curves (10)