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4h55

Crystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose

Method: X-RAY DIFFRACTION Dmax: 60.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Concanavalin-Br

OrganismNot specified

UniProt P55915

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 1–237 Not recorded CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 BDR beta-D-ribofuranose × 4 DBB D-ALPHA-AMINOBUTYRIC ACID × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K Resolution 2.15 Å R-free 0.227

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 4H55 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AZD CONCANAVALIN FROM CANAVALIA BRASILIENSIS Deposited 1997-11-16 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 1–237（237 aa）
Chain B 1–237（237 aa）
Chain C 1–237（237 aa）
Chain D 1–237（237 aa）
Not recorded CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；2 MICRO-L CBR (10 MG/ML) 2 MICRO-L (11-15% PEG 6000, 0.1 M MES PH 6, pH 6.0
Resolution 3.00 Å R-free 0.240
1C57 DIRECT DETERMINATION OF THE POSITIONS OF DEUTERIUM ATOMS OF BOUND WATER IN CONCANAVALIN A BY NEUTRON LAUE CRYSTALLOGRAPHY Deposited 1999-10-26 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 NEUTRON DIFFRACTION
X-ray crystallization conditions pH 6.5；CRYSTALS SELECTED FOR NEUTRON STUDY WERE TRANSFERRED TO A 1ML BUFFERMADE UP OF 99.9% D2O WITH 0.1M NANO3, 0.05M TRIS-ACETATE, 1MM MNCL2 AND 1MM CACL2; PH 6.5.
Resolution 2.40 Å R-free 0.301
1DQ0 Locked, metal-free concanavalin A, a minor species in solution Deposited 1999-12-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–237（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；293 K；2.1 M AMMONIUM SULPHATE, 120 MM SODIUM ACETATE, SOAKING OF LOCKED MNMN CON A CRYSTALS WITH THE METAL CHELATOR EDTA, pH 7.0, temperature 293.0K
Resolution 1.70 Å R-free 0.204
1DQ1 Calcium;Calcium concanavalin A Deposited 1999-12-29 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–237（237 aa）
Not recorded CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；293 K；2.1 M ammonium sulphate, 120 mM sodium acetate, 100 mM calcium, prepared by soaking of locked, metal-free concanavalin A crystals (1DQ0) with calcium, pH 7.0, temperature 293.0K
Resolution 2.15 Å R-free 0.276
1DQ2 Unlocked metal-free concanavalin A Deposited 1999-12-29 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 1–237（237 aa）
Chain B 1–237（237 aa）
Not recorded ACY ACETIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；2 M ammonium sulphate, 100 mM sodium acetate, 3% (w/v) PEG4000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Resolution 2.05 Å R-free 0.279
1DQ4 A transient unlocked concanavalin A structure with MN2+ bound in the transition metal ion binding site S1 and an empty calcium binding site S2 Deposited 1999-12-30 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 1–237（237 aa）
Chain B 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；277 K；2.0 M ammonium sulphate, 100 mM sodium acetate, 3% PEG4000, 7 mM MnCl2, unlocked metal-free concanavalin A crystals were soaked with Mn2+, pH 5.0, temperature 277.0K
Resolution 2.90 Å R-free 0.246
1DQ5 Manganese;Manganese concanavalin A at pH 5.0 Deposited 1999-12-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；277 K；2.0 M ammonium sulphate, 100 mM sodium acetate, 3% PEG4000, 5 mM Mn2+, crystals of unlocked, metal-free con A were soaked with Mn2+, pH 5.0, temperature 277.0K
Resolution 2.00 Å R-free 0.210
1JOJ CONCANAVALIN A-HEXAPEPTIDE COMPLEX Deposited 2001-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–237（237 aa）
Chain B 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.231
1JOJ CONCANAVALIN A-HEXAPEPTIDE COMPLEX Deposited 2001-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–237（237 aa）
Chain D 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.231
1JUI CONCANAVALIN A-CARBOHYDRATE MIMICKING 10-MER PEPTIDE COMPLEX Deposited 2001-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–237（237 aa）
Chain B 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.75 Å R-free 0.222
1JUI CONCANAVALIN A-CARBOHYDRATE MIMICKING 10-MER PEPTIDE COMPLEX Deposited 2001-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–237（237 aa）
Chain D 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.75 Å R-free 0.222
1JYC CONCANAVALIN A/15-mer PEPTIDE COMPLEX Deposited 2001-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–237（237 aa）
Chain B 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.75 Å R-free 0.240
1JYC CONCANAVALIN A/15-mer PEPTIDE COMPLEX Deposited 2001-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–237（237 aa）
Chain D 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.75 Å R-free 0.240
1JYI CONCANAVALIN A/12-MER PEPTIDE COMPLEX Deposited 2001-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–237（237 aa）
Chain B 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.75 Å R-free 0.265
1JYI CONCANAVALIN A/12-MER PEPTIDE COMPLEX Deposited 2001-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–237（237 aa）
Chain D 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.75 Å R-free 0.265
1QDC MAN(APLHA1-6)MAN(ALPHA1-O)METHYL CONCANAVALIN A COMPLEX Deposited 1998-07-14 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 1–237（237 aa）
Chain B 1–237（237 aa）
Chain C 1–237（237 aa）
Chain D 1–237（237 aa）
Not recorded MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；DROP: 5 MICROLITER 7 MG/ML CON A + 5 MICROLITER 7% JEFFAMINE M-600, 10 % PEG 8000, 50 MM NH4COOH, 5MM MGCL2, 25 MM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.00 Å R-free 0.211
3JU9 Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with alpha-aminobutyric acid Deposited 2009-09-14 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–237（237 aa）
Not recorded DBB D-ALPHA-AMINOBUTYRIC ACID × 4 GOL GLYCEROL × 4 CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.10 Å R-free 0.253
4P14 Crystal structure of Canavalia brasiliensis (ConBr) complexed with adenine Deposited 2014-02-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–237（237 aa）
Not recorded CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 ADE ADENINE × 4 GOL GLYCEROL × 8 DBB D-ALPHA-AMINOBUTYRIC ACID × 4 EDO 1,2-ETHANEDIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.00 Å R-free 0.228
4PCR Crystal structure of Canavalia brasiliensis seed lectin (ConBr) complexed with Gamma-Aminobutyric Acid (GABA) Deposited 2014-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–237（237 aa）
Chain D 1–237（237 aa）
Not recorded CA CALCIUM ION × 2 MN MANGANESE (II) ION × 2 IPA ISOPROPYL ALCOHOL × 2 ABU GAMMA-AMINO-BUTANOIC ACID × 3 PEG DI(HYDROXYETHYL)ETHER × 3 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；TRIS 0.1 M pH 9.0, amonium sulfate 2.2 M
Resolution 2.15 Å R-free 0.236
4PCR Crystal structure of Canavalia brasiliensis seed lectin (ConBr) complexed with Gamma-Aminobutyric Acid (GABA) Deposited 2014-04-16 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 A 1–237（237 aa）
Chain D 1–237（237 aa）
Not recorded CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 IPA ISOPROPYL ALCOHOL × 4 ABU GAMMA-AMINO-BUTANOIC ACID × 6 PEG DI(HYDROXYETHYL)ETHER × 6 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；TRIS 0.1 M pH 9.0, amonium sulfate 2.2 M
Resolution 2.15 Å R-free 0.236
6VB8 Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with indole-3-acetic acid Deposited 2019-12-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–237（237 aa）
Not recorded GOL GLYCEROL × 4 CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 CL CHLORIDE ION × 8 DBB D-ALPHA-AMINOBUTYRIC ACID × 4 IAC 1H-INDOL-3-YLACETIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5
Resolution 2.20 Å R-free 0.236
8YJ9 Crystallization Studies of Concanavalin A in-Complex with D-Arabinose Deposited 2024-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–237（237 aa）
Not recorded GOL GLYCEROL × 3 ROR L-ribose × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；Crystallization solution was comprised of sodium acetate (100 mM, pH=5), PEG6000 (5%), and Ammoniun Sulphate (2M) in hanging drop vapor diffusion setup.
Resolution 2.20 Å R-free 0.221
8YYA Crystal Structure of Concanavalin A Complexed with 5-Fluorouracil Deposited 2024-04-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–237（237 aa）
Not recorded URF 5-FLUOROURACIL × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293.5 K；0. 1M Sodium Accetate buffer pH 5.0 , 5% PEG 6000, 2 M Ammonium Sulphate.
Resolution 2.96 Å R-free 0.274
8ZE7 Crystal Structure of Concanavalin A Complexed with Lysine Deposited 2024-05-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–237（237 aa）
Not recorded LYS LYSINE × 1 GOL GLYCEROL × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；2M Ammonium Sulphate, 0.1M Sodium Acetate (pH 5.0), PEG600 (5%), temperature 293.0 K
Resolution 2.22 Å R-free 0.248

19 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CONA_CANBR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–237； UniProt 1–237

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 4h55

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4h55
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4h55
Deposition date deposition_date2012-09-18
Structure title titleCrystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose
Keywords keywordsSugar-binding protein, beta-sandwich, Sugar recognition, Carbohydrate-binding protein, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.75 Å
Radius of gyration Rg (electron density) rg_electron16.46 Å
Forward intensity I(0) i011615800.00
Molecular weight molecular_weight25458.0 kDa
Excluded volume excluded_volume31813 ų
Envelope volume envelope_volume34177 ų
Hydration-shell volume shell_volume17099 ų
Envelope diameter envelope_diameter60.7 Å
Shell Rg shell_rg23.00 Å
Envelope Rg envelope_rg16.94 Å
Shape Rg shape_rg16.43 Å
Total Rg total_rg17.53 Å
Total atoms total_atoms1794
Residues n_residues233
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax60.3 Å
Rg (real space) rg_real17.65 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real1.1620e+07
I(0) uncertainty (real space) i0_real_error1.3390e+05
Rg (reciprocal space) rg_reciprocal17.67 Å
I(0) (reciprocal space) i0_reciprocal11620000.0000
Solution quality estimate total_estimate0.7840
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.209
Kurtosis Kurtosis kurtosis-0.250
Angular range angular_range— – 0.4500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2601000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.735; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4h55a_
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 (1 domains)

Domain ID domain_id4h55A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
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8. Citations (1)

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9. Files and Curves (10)