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1m7l

Solution Structure of the Coiled-Coil Trimerization Domain from Lung Surfactant Protein D

Method: SOLUTION NMR Dmax: 48.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pulmonary surfactant-associated protein D

Homo sapiens

UniProt P35247

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 220–257 Chain B； UniProt 220–257 Chain C； UniProt 220–257 Fragment：Trimeric Coiled-Coil Domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 4.4；303 K NMR sample composition：90% H2O/10% D2O Resolution not provided

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 1M7L 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 method 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
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 method 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 method 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 method 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 method 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 method 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 method 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 method 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
2RIA Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with D-glycero-D-manno-heptose Deposited 2007-10-10 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 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 × 9 289 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
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 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 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 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 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 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 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 1–38； UniProt 220–257 Author chain B； PDBConstruct 1–38； UniProt 220–257 Author chain C； PDBConstruct 1–38； UniProt 220–257

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

SAXS profile for 1m7l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1m7l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1m7l
Deposition date deposition_date2002-07-22
Structure title titleSolution Structure of the Coiled-Coil Trimerization Domain from Lung Surfactant Protein D
Keywords keywordscoiled coil, lung surfactant protein, trimer, ambiguous distance restraints, NMR-spectroscopy, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.28 Å
Radius of gyration Rg (electron density) rg_electron17.79 Å
Forward intensity I(0) i01020170000.00
Molecular weight molecular_weight275060.0 kDa
Excluded volume excluded_volume346140 ų
Envelope volume envelope_volume34679 ų
Hydration-shell volume shell_volume14995 ų
Envelope diameter envelope_diameter71.3 Å
Shell Rg shell_rg26.36 Å
Envelope Rg envelope_rg21.81 Å
Shape Rg shape_rg17.75 Å
Total Rg total_rg18.10 Å
Total atoms total_atoms39060
Residues n_residues2520
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax48.8 Å
Rg (real space) rg_real16.60 Å
Rg uncertainty (real space) rg_real_error0.11 Å
I(0) (real space) i0_real9.8480e+08
I(0) uncertainty (real space) i0_real_error1.0050e+07
Rg (reciprocal space) rg_reciprocal17.51 Å
I(0) (reciprocal space) i0_reciprocal1020000000.0000
Solution quality estimate total_estimate0.6258
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.522
Kurtosis Kurtosis kurtosis-0.405
Angular range angular_range— – 0.4600 Å−1
Current regularization parameter α current_alpha3.2940
Highest regularization parameter α highest_alpha930200.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.740; Stabil: 0.992; Sysdev: 0.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1m7la1
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.1 — Triple coiled coil domain of C-type lectins
Family Family familyh.1.1.1 — Triple coiled coil domain of C-type lectins
Domain ID domain_idd1m7la2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1m7lb1
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.1 — Triple coiled coil domain of C-type lectins
Family Family familyh.1.1.1 — Triple coiled coil domain of C-type lectins
Domain ID domain_idd1m7lb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1m7lc1
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.1 — Triple coiled coil domain of C-type lectins
Family Family familyh.1.1.1 — Triple coiled coil domain of C-type lectins
Domain ID domain_idd1m7lc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id1m7lA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily360 — SFTPD helical domain
Domain ID domain_id1m7lB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily360 — SFTPD helical domain
Domain ID domain_id1m7lC00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily360 — SFTPD helical domain
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8. Citations (1)

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9. Files and Curves (10)