SAXSdb — 1rdk

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

MANNOSE-BINDING PROTEIN-C

Rattus rattus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain 1； UniProt 132–244 Chain 2； UniProt 132–244	Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226)	GAL beta-D-galactopyranose × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.4；pH 7.4	Resolution 1.80 Å R-free 0.265

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 1RDK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BV4 APO-MANNOSE-BINDING PROTEIN-C Deposited 1998-09-22	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 127–244（118 aa） Fragment：SUBTILISIN FRAGMENT Chain B 127–244（118 aa） Fragment：SUBTILISIN FRAGMENT Chain C 127–244（118 aa） Fragment：SUBTILISIN FRAGMENT Chain D 127–244（118 aa） Fragment：SUBTILISIN FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；12% PEG 8000, 100 MM NAMES, PH 6.1, 200 MM LICL, 2 MM EDTA 0.02%, NAN3, pH 6.2	Resolution 1.85 Å R-free 0.256
1KZA Complex of MBP-C and Man-a13-Man Deposited 2002-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661) Chain 2 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661)	Not recorded	MAN alpha-D-mannopyranose × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 8000, Tris-Cl, NaCl, CaCl2, NaN3, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.74 Å R-free 0.235
1KZB Complex of MBP-C and trimannosyl core Deposited 2002-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661) Chain 2 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661)	Not recorded	MAN alpha-D-mannopyranose × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 8000, Tris-Cl, NaCl, CaCl2, NaN3, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.80 Å R-free 0.259
1KZC Complex of MBP-C and high-affinity linear trimannose Deposited 2002-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661) Chain 2 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661)	Not recorded	MAN alpha-D-mannopyranose × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 8000, Tris-Cl, NaCl, CaCl2, NaN3, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.85 Å R-free 0.242
1KZD Complex of MBP-C and GlcNAc-terminated core Deposited 2002-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661) Chain 2 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 8000, Tris-Cl, NaCl, CaCl2, NaN3, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.90 Å R-free 0.239
1KZE Complex of MBP-C and bivalent Man-terminated glycopeptide Deposited 2002-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661) Chain 2 129–243（115 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661)	Not recorded	MAN alpha-D-mannopyranose × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；PEG 8000, Tris-Cl, NaCl, CaCl2, NaN3, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.80 Å R-free 0.243
1RDI MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-L-FUCOPYRANOSIDE Deposited 1995-09-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226) Chain 2 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226)	Not recorded	MFU methyl alpha-L-fucopyranoside × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4, 20% MPD USED AS A CRYOPROTECTANT	Resolution 1.80 Å R-free 0.244
1RDJ MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH BETA-METHYL-L-FUCOPYRANOSIDE Deposited 1995-09-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226) Chain 2 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226)	Not recorded	MFB methyl beta-L-fucopyranoside × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4, 20% MPD USED AS A CRYOPROTECTANT	Resolution 1.80 Å R-free 0.246
1RDL MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-D-MANNOPYRANOSIDE (0.2 M) Deposited 1995-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226) Chain 2 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226)	Not recorded	MMA methyl alpha-D-mannopyranoside × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 1.70 Å R-free 0.230
1RDM MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-D-MANNOPYRANOSIDE (1.3 M) Deposited 1995-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226) Chain 2 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226)	Not recorded	MMA methyl alpha-D-mannopyranoside × 3 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 1.90 Å R-free 0.240
1RDN MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-D-N-ACETYLGLUCOSAMINIDE Deposited 1995-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226) Chain 2 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226)	Not recorded	NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 1.80 Å R-free 0.237
1RDO MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT Deposited 1995-09-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226) Chain 2 132–244（113 aa） Fragment：SUBTILISIN FRAGMENT (RESIDUES 114 - 226)	Not recorded	CA CALCIUM ION × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 1.70 Å R-free 0.238

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MBL2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–113； UniProt 132–244 Author chain 2； PDBConstruct 1–113； UniProt 132–244

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	1rdk
Deposition date deposition_date	1995-09-05
Structure title title	MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH D-GALACTOSE
Keywords keywords	C-TYPE LECTIN, CALCIUM-BINDING PROTEIN, 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	21.54 Å
Radius of gyration Rg (electron density) rg_electron	20.69 Å
Forward intensity I(0) i0	12866400.00
Molecular weight molecular_weight	25485.0 kDa
Excluded volume excluded_volume	31248 Å³
Envelope volume envelope_volume	37077 Å³
Hydration-shell volume shell_volume	16181 Å³
Envelope diameter envelope_diameter	71.3 Å
Shell Rg shell_rg	25.28 Å
Envelope Rg envelope_rg	20.79 Å
Shape Rg shape_rg	20.71 Å
Total Rg total_rg	21.27 Å
Total atoms total_atoms	1776
Residues n_residues	223
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	71.3 Å
Rg (real space) rg_real	21.71 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	1.2870e+07
I(0) uncertainty (real space) i0_real_error	1.9860e+05
Rg (reciprocal space) rg_reciprocal	21.68 Å
I(0) (reciprocal space) i0_reciprocal	12870000.0000
Solution quality estimate total_estimate	0.8408
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.9 Å
Skewness Skewness skewness	0.476
Kurtosis Kurtosis kurtosis	-0.517
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3332000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.720; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.784; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	MANNOSE-BINDING PROTEIN-C
Molecular weight formula_weight	12675.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2
Atom count atom_count	2077

KKYFMSSVRRMPLNRAKALCSELQGTVATPRNAEENRAIQNVAKDVAFLGITDQRTENVFEDLTGNRVRYTNWNEGEPNNVGSGENCVVLLTNGKWNDVPCSDSFLVVCEFSD

来源 Source

来源生物 organism	Rattus rattus
通用名 common_name	black rat
NCBI Class编号 ncbi_taxonomy_id	10117
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	beta-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	286

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1rdk1_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1rdk2_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (2 domains)

Domain ID domain_id	1rdk100
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1rdk200
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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8. Citations (5)

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Unit-cell length a length_a	60.700 Å
Unit-cell length b length_b	75.300 Å
Unit-cell length c length_c	57.400 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	1.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2650

fit	/app/data/saxs_computation/rd/1rdk/1rdk.fit
pddf	/app/data/pr_computation/rd/1rdk/1rdk.pr.out
profile	/app/data/saxs_computation/rd/1rdk/1rdk.dat

MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH D-GALACTOSE

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

MANNOSE-BINDING PROTEIN-C

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