SAXSdb — 1c39

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

CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR

Bos taurus

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 × 2 其他Polymer 4 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 31–182 Chain B； UniProt 31–182	Fragment：EXTRACYTOPLASMIC DOMAIN Mutation：N31Q, N57Q, N68Q, N87Q	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 6-O-phosphono-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose × 2 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.4；pH 6.40	Resolution 1.85 Å R-free 0.246

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 1C39	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KEO TWISTS AND TURNS OF THE CD-MPR: LIGAND-BOUND VERSUS LIGAND-FREE RECEPTOR Deposited 2001-11-16	Different construct 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 29–182（154 aa） Fragment：(Residues 29-182) Chain B 29–182（154 aa） Fragment：(Residues 29-182)	Mutation：N31Q, N57Q, N68Q, N87Q Mutation：N31Q, N57Q, N68Q, N87Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；25% PEG 5000 monomethyl ether, 0.2M ammonium acetate, 0.1M cacodoylate, 150 mM Nacl, 50 mM imidazole (pH=6.5), 10 mM Manganese chloride, 5 mM beta-glycerophosphate, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.20 Å R-free 0.248
1M6P EXTRACYTOPLASMIC DOMAIN OF BOVINE CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR Deposited 1998-04-19	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 31–182（152 aa） Fragment：EXTRACYTOPLASMIC DOMAIN Chain B 31–182（152 aa） Fragment：EXTRACYTOPLASMIC DOMAIN	Mutation：N31Q, N57Q, N68Q, N87Q Mutation：N31Q, N57Q, N68Q, N87Q	MN MANGANESE (II) ION × 2 M6P 6-O-phosphono-alpha-D-mannopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.80 Å R-free 0.276
2RL7 Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 4.8 Deposited 2007-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–182（154 aa） Chain B 29–182（154 aa）	Mutation：N31Q, N57Q, N68Q, N87Q Mutation：N31Q, N57Q, N68Q, N87Q	GOL GLYCEROL × 1 ACT ACETATE ION × 2 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.8；277 K；0.05M cacodylate, 30% PEG5000MME, 0.2M ammonium sulfate, 0.09mM TritonX-100, pH 4.8, VAPOR DIFFUSION, temperature 277K	Resolution 2.00 Å R-free 0.257
2RL7 Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 4.8 Deposited 2007-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 29–182（154 aa） Chain D 29–182（154 aa）	Mutation：N31Q, N57Q, N68Q, N87Q Mutation：N31Q, N57Q, N68Q, N87Q	GOL GLYCEROL × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.8；277 K；0.05M cacodylate, 30% PEG5000MME, 0.2M ammonium sulfate, 0.09mM TritonX-100, pH 4.8, VAPOR DIFFUSION, temperature 277K	Resolution 2.00 Å R-free 0.257
2RL8 Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to M6P Deposited 2007-10-18	Different construct 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 29–182（154 aa） Chain B 29–182（154 aa）	Mutation：N31Q, N57Q, N68Q, N87Q Mutation：N31Q, N57Q, N68Q, N87Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MN MANGANESE (II) ION × 2 M6D 6-O-phosphono-beta-D-mannopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；292 K；0.1M cacodylate, 25% PEG5000MME, 0.2M ammonium sulfate, pH 6.5, vapor diffusion, temperature 292K	Resolution 1.45 Å R-free 0.237
2RL9 Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to trimannoside Deposited 2007-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–182（154 aa） Chain B 29–182（154 aa）	Mutation：N31Q, N57Q, N68Q, N87Q Mutation：N31Q, N57Q, N68Q, N87Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；292 K；0.1M cacodylate, 25% PEG5000MME, 0.2M ammonium sulfate, pH 6.5, vapor diffusion, temperature 292K	Resolution 2.40 Å R-free 0.265
2RLB Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to M6P in absence of Mn Deposited 2007-10-18	Different construct 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 29–182（154 aa） Chain B 29–182（154 aa）	Mutation：N31Q, N57Q, N68Q, N87Q Mutation：N31Q, N57Q, N68Q, N87Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 M6D 6-O-phosphono-beta-D-mannopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1M cacodylate, 25% PEG5000MME, 0.2M ammonium sulfate, pH 6.5, temperature 292K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.75 Å R-free 0.229
3CY4 Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 7.4 Deposited 2008-04-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–182（154 aa） Chain B 29–182（154 aa）	Mutation：N31Q, N57Q, N68Q, N87Q Mutation：N31Q, N57Q, N68Q, N87Q	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；292 K；0.1M cacodylate, 25% PEG5000MME, 0.2M ammonium sulfate, pH 7.4, VAPOR DIFFUSION, temperature 292K	Resolution 1.51 Å R-free 0.229
3K41 Crystal structure of sCD-MPR mutant E19Q/K137M bound to Man-6-P Deposited 2009-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–182（154 aa） Fragment：UNP residues 29-182 Chain B 29–182（154 aa） Fragment：UNP residues 29-182	Mutation：E19Q, K137M, N31Q, N57Q, N68Q, N87Q Mutation：E19Q, K137M, N31Q, N57Q, N68Q, N87Q	M6D 6-O-phosphono-beta-D-mannopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100 mM sodium cacodylate, pH 6.5;25% PEG 2000MME; 0.2M ammonium acetate; 0.025M OBG, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.90 Å R-free 0.255
3K42 Crystal structure of sCD-MPR mutant E19Q/K137M pH 7.0 Deposited 2009-10-05	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 29–182（154 aa） Fragment：UNP residues 29-182 Chain B 29–182（154 aa） Fragment：UNP residues 29-182	Mutation：E19Q, K137M, N31Q, N57Q, N68Q, N87Q Mutation：E19Q, K137M, N31Q, N57Q, N68Q, N87Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1GP SN-GLYCEROL-1-PHOSPHATE × 2 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1M HEPES pH 7.0, 3M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.30 Å R-free 0.249
3K42 Crystal structure of sCD-MPR mutant E19Q/K137M pH 7.0 Deposited 2009-10-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–182（154 aa） Fragment：UNP residues 29-182 Chain B 29–182（154 aa） Fragment：UNP residues 29-182	Mutation：E19Q, K137M, N31Q, N57Q, N68Q, N87Q Mutation：E19Q, K137M, N31Q, N57Q, N68Q, N87Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1GP SN-GLYCEROL-1-PHOSPHATE × 2 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1M HEPES pH 7.0, 3M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.30 Å R-free 0.249
3K43 Crystal structure of sCD-MPR mutant E19Q/K137M pH 6.5 Deposited 2009-10-05	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 29–182（154 aa） Fragment：UNP residues 29-182 Chain B 29–182（154 aa） Fragment：UNP residues 29-182	Mutation：E19Q, K137M,N31Q, N57Q, N68Q, N87Q Mutation：E19Q, K137M,N31Q, N57Q, N68Q, N87Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 3 ACT ACETATE ION × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1M sodium cacodylate, 3M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.199

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

View Construct and Data Evidence

UniProt name	MPRD_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–152； UniProt 31–182 Author chain B； PDBConstruct 1–152； UniProt 31–182

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	1c39
Deposition date deposition_date	1999-07-25
Structure title title	STRUCTURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND TO PENTAMANNOSYL PHOSPHATE
Keywords keywords	RECEPTOR, CATION DEPENDENT MANNOSE 6-PHOSPHATE, P-TYPE LECT TRANSPORT, SIGNALING PROTEIN; SIGNALING PROTEIN
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	21.16 Å
Radius of gyration Rg (electron density) rg_electron	19.90 Å
Forward intensity I(0) i0	25715000.00
Molecular weight molecular_weight	36478.0 kDa
Excluded volume excluded_volume	44674 Å³
Envelope volume envelope_volume	53437 Å³
Hydration-shell volume shell_volume	22135 Å³
Envelope diameter envelope_diameter	68.4 Å
Shell Rg shell_rg	26.54 Å
Envelope Rg envelope_rg	20.06 Å
Shape Rg shape_rg	19.87 Å
Total Rg total_rg	20.81 Å
Total atoms total_atoms	2540
Residues n_residues	304
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	66.9 Å
Rg (real space) rg_real	21.03 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	2.5710e+07
I(0) uncertainty (real space) i0_real_error	3.2410e+05
Rg (reciprocal space) rg_reciprocal	21.05 Å
I(0) (reciprocal space) i0_reciprocal	25720000.0000
Solution quality estimate total_estimate	0.8986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.140
Kurtosis Kurtosis kurtosis	-0.413
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3600000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.997

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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	CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
Molecular weight formula_weight	17213.4 kDa
Mutation mutation	N31Q, N57Q, N68Q, N87Q
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2711

EKTCDLVGEKGKESEKELALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	6-O-phosphono-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose
Molecular weight formula_weight	584.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1c39a_
Class class	b — All beta proteins
Fold Fold fold	b.64 — Mannose 6-phosphate receptor domain
Superfamily Superfamily superfamily	b.64.1 — Mannose 6-phosphate receptor domain
Family Family family	b.64.1.1 — Mannose 6-phosphate receptor domain

Domain ID domain_id	d1c39b_
Class class	b — All beta proteins
Fold Fold fold	b.64 — Mannose 6-phosphate receptor domain
Superfamily Superfamily superfamily	b.64.1 — Mannose 6-phosphate receptor domain
Family Family family	b.64.1.1 — Mannose 6-phosphate receptor domain

CATH v4.4 (2 domains)

Domain ID domain_id	1c39A00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	130 — Cation-dependent Mannose-6-phosphate Receptor; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-6-phosphate receptor binding domain

Domain ID domain_id	1c39B00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	130 — Cation-dependent Mannose-6-phosphate Receptor; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-6-phosphate receptor binding domain

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8. Citations (2)

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Unit-cell length a length_a	42.840 Å
Unit-cell length b length_b	79.310 Å
Unit-cell length c length_c	55.570 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2460

fit	/app/data/saxs_computation/c3/1c39/1c39.fit
pddf	/app/data/pr_computation/c3/1c39/1c39.pr.out
profile	/app/data/saxs_computation/c3/1c39/1c39.dat

STRUCTURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND TO PENTAMANNOSYL PHOSPHATE

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

CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR

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