2ria

Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose

Method: X-RAY DIFFRACTION D_max: 76.1 Å Quality: GOOD

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

Pulmonary surfactant-associated protein D

Homo sapiens

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 223–375 Chain B； UniProt 223–375 Chain C； UniProt 223–375	Fragment：neck and carbohydrate recognition domain	CA CALCIUM ION × 9 289 D-glycero-alpha-D-manno-heptopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.237

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 2RIA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B08 LUNG SURFACTANT PROTEIN D (SP-D) (FRAGMENT) Deposited 1998-11-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 218–375（158 aa） Fragment：TRIMERIC FRAGMENT CONSISTING OF LECTIN DOMAINS AND ALPHA-HELICAL COILED-COIL Chain B 218–375（158 aa） Fragment：TRIMERIC FRAGMENT CONSISTING OF LECTIN DOMAINS AND ALPHA-HELICAL COILED-COIL Chain C 218–375（158 aa） Fragment：TRIMERIC FRAGMENT CONSISTING OF LECTIN DOMAINS AND ALPHA-HELICAL COILED-COIL	Not recorded	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；AN EQUAL AMOUNT OF PROTEIN SOLUTION (8 MG/ML PROTEIN IN 10 MM TRIS 140 MM NACL 1MM CACL2 0.02% (W/V) NAN3 PH 7.5) AND PRECIPITANT BUFFER (10-20% (W/V) PEG 20000 IN 100 MM TRIS PH 6-8) WERE MIXED AND VAPOR EQUILIBRATED AGAINST THE LATTER., pH 7.00	Resolution 2.30 Å R-free 0.271
1M7L Solution Structure of the Coiled-Coil Trimerization Domain from Lung Surfactant Protein D Deposited 2002-07-22	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 220–257（38 aa） Fragment：Trimeric Coiled-Coil Domain Chain B 220–257（38 aa） Fragment：Trimeric Coiled-Coil Domain Chain C 220–257（38 aa） Fragment：Trimeric Coiled-Coil Domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.4；303 K NMR sample composition 90% H2O/10% D2O	Resolution not provided
1PW9 High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D Deposited 2003-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 199–375（177 aa） Fragment：Residues 179-355 Chain B 199–375（177 aa） Fragment：Residues 179-355 Chain C 199–375（177 aa） Fragment：Residues 179-355	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；PEG 4000, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 1.60 Å R-free 0.249
1PWB High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D with maltose Deposited 2003-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 199–375（177 aa） Fragment：recombinant fragment Chain B 199–375（177 aa） Fragment：recombinant fragment Chain C 199–375（177 aa） Fragment：recombinant fragment	Not recorded	CA CALCIUM ION × 9 GLC alpha-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG 10000, Tris, maltose, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.40 Å R-free 0.228
2GGU crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with maltotriose Deposited 2006-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：trimeric neck and carbohydrate recognition domain Chain B 223–375（153 aa） Fragment：trimeric neck and carbohydrate recognition domain Chain C 223–375（153 aa） Fragment：trimeric neck and carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；12% PEG 8000, 150mM NaCl, 10mM CaCl2, 100mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.90 Å R-free 0.248
2GGX Crystal structure of the trimer neck and carbohydrate recognition domain of human surfactant protein D in complex with p-nitrophenyl maltoside Deposited 2006-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：Trimeric neck and carbohydrate recognition domain Chain B 223–375（153 aa） Fragment：Trimeric neck and carbohydrate recognition domain Chain C 223–375（153 aa） Fragment：Trimeric neck and carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9 NPJ 4-NITROPHENYL 4-O-ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GALACTOPYRANOSIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；12% PEG 8000, 150mM NaCl, 10mM CaCl2, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.90 Å R-free 0.238
2ORJ crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with N-acetyl mannosamine Deposited 2007-02-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：head and neck domain Chain B 223–375（153 aa） Fragment：head and neck domain Chain C 223–375（153 aa） Fragment：head and neck domain	Not recorded	CA CALCIUM ION × 9 BM3 2-acetamido-2-deoxy-alpha-D-mannopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150mM NaCl, 10mM CaCl2, 12% PEG 8000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.205
2ORK crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with inositol-1-phosphate Deposited 2007-02-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：head and neck domain Chain B 223–375（153 aa） Fragment：head and neck domain Chain C 223–375（153 aa） Fragment：head and neck domain	Not recorded	CA CALCIUM ION × 9 IPD D-MYO-INOSITOL-1-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150mM NaCl, 10mM CaCl2, 12% PEG 8000, 100mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.89 Å R-free 0.226
2OS9 crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with myoinositol Deposited 2007-02-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：head and neck domain Chain B 223–375（153 aa） Fragment：head and neck domain Chain C 223–375（153 aa） Fragment：head and neck domain	Not recorded	CA CALCIUM ION × 9 INS 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150mM NaCl, 10mM CaCl2, 12% PEG 8000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.70 Å R-free 0.223
2RIB Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with L-glycero-D-manno-heptose Deposited 2007-10-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：neck and carbohydrate recognition domain Chain B 223–375（153 aa） Fragment：neck and carbohydrate recognition domain Chain C 223–375（153 aa） Fragment：neck and carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9 GMH L-glycero-alpha-D-manno-heptopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES , PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.204
2RIC Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with L-glycero-D-manno-heptopyranosyl-(1-3)-L-glycero-D-manno-heptopyranose Deposited 2007-10-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：neck and carbohydrate recognition domain Chain B 223–375（153 aa） Fragment：neck and carbohydrate recognition domain Chain C 223–375（153 aa） Fragment：neck and carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9 GMH L-glycero-alpha-D-manno-heptopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES , PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.230
2RID Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with Allyl 7-O-carbamoyl-L-glycero-D-manno-heptopyranoside Deposited 2007-10-10	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：neck and carbohydrate recognition domain Chain B 223–375（153 aa） Fragment：neck and carbohydrate recognition domain Chain C 223–375（153 aa） Fragment：neck and carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9 291 prop-2-en-1-yl 7-O-carbamoyl-L-glycero-alpha-D-manno-heptopyranoside × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.232
2RIE Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with 2-deoxy-L-glycero-D-manno-heptose Deposited 2007-10-10	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：neck and carbohydrate recognition domain Chain B 223–375（153 aa） Fragment：neck and carbohydrate recognition domain Chain C 223–375（153 aa） Fragment：neck and carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9 293 2-deoxy-beta-L-galacto-heptopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；12% PEG 8000, 150MM NACL, 10MM CACL2, 100MM HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.60 Å R-free 0.212
3DBZ human surfactant protein D Deposited 2008-06-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：Head and Neck Domain, UNP residues 223-375 Chain B 223–375（153 aa） Fragment：Head and Neck Domain, UNP residues 223-375 Chain C 223–375（153 aa） Fragment：Head and Neck Domain, UNP residues 223-375	Not recorded	CA CALCIUM ION × 9 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150MM NACL, 10MM CACL2, 12% PEG8000, 100MM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.202
3G81 Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with alpha methyl mannoside Deposited 2009-02-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：UNP residues 223-375 Chain B 223–375（153 aa） Fragment：UNP residues 223-375 Chain C 223–375（153 aa） Fragment：UNP residues 223-375	Not recorded	CA CALCIUM ION × 9 MMA methyl alpha-D-mannopyranoside × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150MM NACL, 10MM CACL2, 12% PEG 8000, 100MM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.200
3G83 Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with alpha 1,2 dimannose. Deposited 2009-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：UNP residues 223-375 Chain B 223–375（153 aa） Fragment：UNP residues 223-375 Chain C 223–375（153 aa） Fragment：UNP residues 223-375	Not recorded	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150MM NACL, 10MM CACL2, 12% PEG 8000, 100MM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.90 Å R-free 0.215
3G84 Crystal structure of the trimeric neck and carbohydrate recognition domain of R343V mutant of human surfactant protein D in complex with alpha 1,2 dimannose. Deposited 2009-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 223–375（153 aa） Fragment：UNP residues 223-375 Chain B 223–375（153 aa） Fragment：UNP residues 223-375 Chain C 223–375（153 aa） Fragment：UNP residues 223-375	Mutation：R343V Mutation：R343V Mutation：R343V	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；150MM NACL, 10MM CACL2, 12% PEG 8000, 100MM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.191
3IKN Crystal structure of galactose bound trimeric human lung surfactant protein D Deposited 2009-08-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 199–375（177 aa） Fragment：UNP residues 199-375 Chain B 199–375（177 aa） Fragment：UNP residues 199-375 Chain C 199–375（177 aa） Fragment：UNP residues 199-375	Mutation：P180S Mutation：P180S Mutation：P180S	CA CALCIUM ION × 10 GAL beta-D-galactopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.215
3IKP Crystal structure of inositol phosphate bound trimeric human lung surfactant protein D Deposited 2009-08-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 199–375（177 aa） Fragment：UNP residues 199-375 Chain B 199–375（177 aa） Fragment：UNP residues 199-375 Chain C 199–375（177 aa） Fragment：UNP residues 199-375	Mutation：P180S Mutation：P180S Mutation：P180S	CA CALCIUM ION × 10 IPD D-MYO-INOSITOL-1-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.75 Å R-free 0.213
3IKQ Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D Deposited 2009-08-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 199–375（177 aa） Fragment：UNP residues 199-375 Chain B 199–375（177 aa） Fragment：UNP residues 199-375 Chain C 199–375（177 aa） Fragment：UNP residues 199-375	Mutation：P180S Mutation：P180S Mutation：P180S	CA CALCIUM ION × 10 MAN alpha-D-mannopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.25 Å R-free 0.239
3IKR Crystal structure of alpha 1-4 mannobiose bound trimeric human lung surfactant protein D Deposited 2009-08-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 199–375（177 aa） Fragment：UNP residues 199-375 Chain B 199–375（177 aa） Fragment：UNP residues 199-375 Chain C 199–375（177 aa） Fragment：UNP residues 199-375	Mutation：P180S Mutation：P180S Mutation：P180S	CA CALCIUM ION × 10 MAN alpha-D-mannopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.65 Å R-free 0.212
4E52 Crystal structure of Haemophilus Eagan 4A polysaccharide bound human lung surfactant protein D Deposited 2012-03-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 201–375（175 aa） Fragment：carbohydrate recognition domain Chain B 201–375（175 aa） Fragment：carbohydrate recognition domain Chain C 201–375（175 aa） Fragment：carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 4000, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.210
4M17 Crystal Structure of Surfactant Protein-D D325A/R343V mutant Deposited 2013-08-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain B 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain C 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375)	Mutation：D325A/R343V Mutation：D325A/R343V Mutation：D325A/R343V	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.188
4M17 Crystal Structure of Surfactant Protein-D D325A/R343V mutant Deposited 2013-08-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain E 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain F 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375)	Mutation：D325A/R343V Mutation：D325A/R343V Mutation：D325A/R343V	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.188
4M17 Crystal Structure of Surfactant Protein-D D325A/R343V mutant Deposited 2013-08-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain G 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain H 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain I 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375)	Mutation：D325A/R343V Mutation：D325A/R343V Mutation：D325A/R343V	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.188
4M17 Crystal Structure of Surfactant Protein-D D325A/R343V mutant Deposited 2013-08-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain J 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain K 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain L 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375)	Mutation：D325A/R343V Mutation：D325A/R343V Mutation：D325A/R343V	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.10 Å R-free 0.188
4M18 Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man) Deposited 2013-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain B 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain C 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375)	Mutation：D325A/R343V Mutation：D325A/R343V Mutation：D325A/R343V	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.20 Å R-free 0.222
4M18 Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man) Deposited 2013-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain E 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain F 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375)	Mutation：D325A/R343V Mutation：D325A/R343V Mutation：D325A/R343V	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.20 Å R-free 0.222
4M18 Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man) Deposited 2013-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain G 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain H 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain I 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375)	Mutation：D325A/R343V Mutation：D325A/R343V Mutation：D325A/R343V	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.20 Å R-free 0.222
4M18 Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man) Deposited 2013-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain J 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain K 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375) Chain L 229–375（147 aa） Fragment：neck and carbohydrate recognition domain (UNP residues 229-375)	Mutation：D325A/R343V Mutation：D325A/R343V Mutation：D325A/R343V	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；Purified D325A+R343V (12-15 mg/mL in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10 mM calcium acetate) + reservoir solution (0.1 M HEPES, pH 7.5, 0.25 M sodium chloride, 20-22% w/v PEG3350), VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.20 Å R-free 0.222
5OXR Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R7 oligosaccharide Deposited 2017-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain B 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain C 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris pH 7.0, 16% PEG 10000	Resolution 1.75 Å R-free 0.196
5OXS Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R5 oligosaccharide Deposited 2017-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain B 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain C 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris pH 8.0, 16% PEG 6000	Resolution 1.65 Å R-free 0.187
9QVU Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepI-(1,5)-KdoI ligand Deposited 2025-04-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain B 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain C 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9 GMH L-glycero-alpha-D-manno-heptopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；16% PEG 4000 and 0.1 M Tris pH 8.0	Resolution 1.75 Å R-free 0.206
9QW2 Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepII-HepI-PhosI ligand Deposited 2025-04-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain B 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain C 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；16% PEG 4000 and 0.1 M Tris pH 8.0	Resolution 1.92 Å R-free 0.212
9QW3 Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepIII-HepII-HepI ligand Deposited 2025-04-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain B 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain C 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9 A1JBO ~{N}-[4-[2-[(2~{S},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxyethyl]phenyl]-2,2,2-tris(fluoranyl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；16% PEG 4000 and 0.1 M Tris pH 8.0	Resolution 1.63 Å R-free 0.199
9QW4 Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic PhosII-HepII-HepI ligand Deposited 2025-04-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain B 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain Chain C 201–375（175 aa） Fragment：Trimeric neck + carbohydrate recognition domain	Not recorded	CA CALCIUM ION × 9 A1JBS [(2~{R},3~{S},4~{R},5~{S},6~{S})-2-[(1~{S})-1,2-bis(oxidanyl)ethyl]-6-[(2~{R},3~{R},4~{S},5~{S},6~{S})-2-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,5-bis(oxidanyl)-6-[2-[4-[2,2,2-tris(fluoranyl)ethanoylamino]phenyl]ethoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate × 1 GMH L-glycero-alpha-D-manno-heptopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；16% PEG 4000 and 0.1 M Tris pH 8.0	Resolution 1.85 Å R-free 0.201

30 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SFTPD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–160； UniProt 223–375 Author chain B； PDBConstruct 8–160； UniProt 223–375 Author chain C； PDBConstruct 8–160； UniProt 223–375

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ria
Deposition date deposition_date	2007-10-10
Structure title title	Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose
Keywords keywords	SURFACTANT PROTEIN; CARBOHYDRATE RECOGNITION; DOMAIN TRIMERIC, SUGAR BINDING PROTEIN; 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	25.98 Å
Radius of gyration Rg (electron density) rg_electron	24.63 Å
Forward intensity I(0) i0	41213100.00
Molecular weight molecular_weight	48501.0 kDa
Excluded volume excluded_volume	60173 Å³
Envelope volume envelope_volume	71473 Å³
Hydration-shell volume shell_volume	25018 Å³
Envelope diameter envelope_diameter	75.2 Å
Shell Rg shell_rg	31.15 Å
Envelope Rg envelope_rg	24.69 Å
Shape Rg shape_rg	24.58 Å
Total Rg total_rg	25.53 Å
Total atoms total_atoms	3396
Residues n_residues	438
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	76.1 Å
Rg (real space) rg_real	25.85 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	4.1210e+07
I(0) uncertainty (real space) i0_real_error	6.1280e+05
Rg (reciprocal space) rg_reciprocal	25.90 Å
I(0) (reciprocal space) i0_reciprocal	41210000.0000
Solution quality estimate total_estimate	0.8398
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.7 Å
Skewness Skewness skewness	0.016
Kurtosis Kurtosis kurtosis	-0.802
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12460000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Pulmonary surfactant-associated protein D
Molecular weight formula_weight	17272.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3772

AMADIGSDVASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	D-glycero-alpha-D-manno-heptopyranose
Molecular weight formula_weight	210.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	376

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2riaa1
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.169.1.0 — automated matches

Domain ID domain_id	d2riaa2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.1 — Triple coiled coil domain of C-type lectins
Family Family family	h.1.1.1 — Triple coiled coil domain of C-type lectins

Domain ID domain_id	d2riab1
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.169.1.0 — automated matches

Domain ID domain_id	d2riab2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.1 — Triple coiled coil domain of C-type lectins
Family Family family	h.1.1.1 — Triple coiled coil domain of C-type lectins

Domain ID domain_id	d2riac1
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.169.1.0 — automated matches

Domain ID domain_id	d2riac2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.1 — Triple coiled coil domain of C-type lectins
Family Family family	h.1.1.1 — Triple coiled coil domain of C-type lectins

CATH v4.4 (3 domains)

Domain ID domain_id	2riaA00
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	2riaB00
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	2riaC00
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 (1)

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Unit-cell length a length_a	55.414 Å
Unit-cell length b length_b	108.606 Å
Unit-cell length c length_c	55.548 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2090
R_free r_free	0.2370

fit	/app/data/saxs_computation/ri/2ria/2ria.fit
pddf	/app/data/pr_computation/ri/2ria/2ria.pr.out
profile	/app/data/saxs_computation/ri/2ria/2ria.dat