SAXSdb — 1qdc

▼

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

PROTEIN (CONCANAVALIN A)

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	Other combination Homooligomer Protein × 4 其他Polymer 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–237 Chain B； UniProt 1–237 Chain C； UniProt 1–237 Chain D； UniProt 1–237	Not recorded	alpha-D-mannopyranose-(1-6)-methyl alpha-D-mannopyranoside × 4 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

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 1QDC	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 oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 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 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 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 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 oligomeric state 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 oligomeric state 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 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 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
3JU9 Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with alpha-aminobutyric acid Deposited 2009-09-14	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 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
4H55 Crystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose Deposited 2012-09-18	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 1–237（237 aa）	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
4P14 Crystal structure of Canavalia brasiliensis (ConBr) complexed with adenine Deposited 2014-02-24	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 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 oligomeric state 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 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 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 Author chain B； PDBConstruct 1–237； UniProt 1–237 Author chain C； PDBConstruct 1–237； UniProt 1–237 Author chain D； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1qdc
Deposition date deposition_date	1998-07-14
Structure title title	MAN(APLHA1-6)MAN(ALPHA1-O)METHYL CONCANAVALIN A COMPLEX
Keywords keywords	PLANT LECTIN, CARBOHYDRATE BINDING, DIMANNOSE, CONCANAVALIN A, 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	30.37 Å
Radius of gyration Rg (electron density) rg_electron	28.95 Å
Forward intensity I(0) i0	173483000.00
Molecular weight molecular_weight	104210.0 kDa
Excluded volume excluded_volume	129910 Å³
Envelope volume envelope_volume	155210 Å³
Hydration-shell volume shell_volume	43557 Å³
Envelope diameter envelope_diameter	88.4 Å
Shell Rg shell_rg	37.37 Å
Envelope Rg envelope_rg	28.80 Å
Shape Rg shape_rg	28.89 Å
Total Rg total_rg	29.84 Å
Total atoms total_atoms	7341
Residues n_residues	948
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	89.5 Å
Rg (real space) rg_real	30.14 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.7350e+08
I(0) uncertainty (real space) i0_real_error	2.4760e+06
Rg (reciprocal space) rg_reciprocal	30.24 Å
I(0) (reciprocal space) i0_reciprocal	173500000.0000
Solution quality estimate total_estimate	0.9108
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	39.6 Å
Skewness Skewness skewness	0.003
Kurtosis Kurtosis kurtosis	-0.687
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26340000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.953

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PROTEIN (CONCANAVALIN A)
Molecular weight formula_weight	25622.4 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7727

ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVDKRLSAVVSYPNADSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-6)-methyl alpha-D-mannopyranoside
Molecular weight formula_weight	356.3 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	386

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1qdca_
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	d1qdcb_
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	d1qdcc_
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	d1qdcd_
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 (4 domains)

Domain ID domain_id	1qdcA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1qdcB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1qdcC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1qdcD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

▶

8. Citations (4)

▶

Unit-cell length a length_a	69.510 Å
Unit-cell length b length_b	117.030 Å
Unit-cell length c length_c	120.920 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	16

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.1752
R_free r_free	0.2110

fit	/app/data/saxs_computation/qd/1qdc/1qdc.fit
pddf	/app/data/pr_computation/qd/1qdc/1qdc.pr.out
profile	/app/data/saxs_computation/qd/1qdc/1qdc.dat

MAN(APLHA1-6)MAN(ALPHA1-O)METHYL CONCANAVALIN A COMPLEX

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

PROTEIN (CONCANAVALIN A)

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