SAXSdb — 3k41

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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 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 29–182 Chain B； UniProt 29–182	Fragment：UNP residues 29-182 Mutation：E19Q, K137M, N31Q, N57Q, N68Q, N87Q	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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

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 3K41	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C39 STRUCTURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND TO PENTAMANNOSYL PHOSPHATE Deposited 1999-07-25	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 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	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；pH 6.40	Resolution 1.85 Å R-free 0.246
1KEO TWISTS AND TURNS OF THE CD-MPR: LIGAND-BOUND VERSUS LIGAND-FREE RECEPTOR Deposited 2001-11-16	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 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 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 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 mutation/modification 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 mutation/modification 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 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） 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 mutation/modification 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 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） 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 mutation/modification 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
3K42 Crystal structure of sCD-MPR mutant E19Q/K137M pH 7.0 Deposited 2009-10-05	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 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 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 1–154； UniProt 29–182 Author chain B； PDBConstruct 1–154； UniProt 29–182

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	3k41
Deposition date deposition_date	2009-10-05
Structure title title	Crystal structure of sCD-MPR mutant E19Q/K137M bound to Man-6-P
Keywords keywords	;transport, lysosome, mannose, receptor, sugar binding, Glycoprotein, Membrane, Phosphoprotein, Transmembrane, Protein transport, sugar binding protein ;; Protein transport, sugar binding 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	20.42 Å
Radius of gyration Rg (electron density) rg_electron	19.18 Å
Forward intensity I(0) i0	23838000.00
Molecular weight molecular_weight	35127.0 kDa
Excluded volume excluded_volume	43092 Å³
Envelope volume envelope_volume	50911 Å³
Hydration-shell volume shell_volume	21732 Å³
Envelope diameter envelope_diameter	65.2 Å
Shell Rg shell_rg	26.01 Å
Envelope Rg envelope_rg	19.43 Å
Shape Rg shape_rg	19.16 Å
Total Rg total_rg	20.12 Å
Total atoms total_atoms	2450
Residues n_residues	296
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	63.3 Å
Rg (real space) rg_real	20.29 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	2.3840e+07
I(0) uncertainty (real space) i0_real_error	3.1650e+05
Rg (reciprocal space) rg_reciprocal	20.32 Å
I(0) (reciprocal space) i0_reciprocal	23840000.0000
Solution quality estimate total_estimate	0.9001
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3402000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.991

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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	18273.5 kDa
Mutation mutation	E19Q, K137M, 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	2611

TEEKTCDLVGEKGKESEKQLALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGMVQDCFYLFEMDSSLACSHHHHHH

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	bovine,cow,domestic cattle,domestic cow
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Pichia Pastoris

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 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	1

Entity 4 Entity 4 non-polymer

Description description	6-O-phosphono-beta-D-mannopyranose
Molecular weight formula_weight	260.1 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	161

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3k41a_
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	d3k41b_
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	3k41A00
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	3k41B00
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 (1)

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Unit-cell length a length_a	53.234 Å
Unit-cell length b length_b	77.112 Å
Unit-cell length c length_c	79.903 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	1.900 Å
Low-resolution limit resolution_low	38.560 Å
R factor r_factor	—
R_work r_work	0.2160
R_free r_free	0.2550

fit	/app/data/saxs_computation/k4/3k41/3k41.fit
pddf	/app/data/pr_computation/k4/3k41/3k41.pr.out
profile	/app/data/saxs_computation/k4/3k41/3k41.dat

Crystal structure of sCD-MPR mutant E19Q/K137M bound to Man-6-P

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