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- PDB-3ikn: Crystal structure of galactose bound trimeric human lung surfacta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ikn | ||||||
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Title | Crystal structure of galactose bound trimeric human lung surfactant protein D | ||||||
![]() | Pulmonary surfactant-associated protein D | ||||||
![]() | SUGAR BINDING PROTEIN / Trimeric recombinant fragment / neck+CRD / Collagen / Disulfide bond / Extracellular matrix / Gaseous exchange / Glycoprotein / Hydroxylation / Lectin / Secreted / Surface film | ||||||
Function / homology | ![]() Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer ...Toll Like Receptor TLR1:TLR2 Cascade / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / extracellular matrix structural constituent conferring tensile strength / Toll Like Receptor 4 (TLR4) Cascade / clathrin-coated endocytic vesicle / respiratory gaseous exchange by respiratory system / Regulation of TLR by endogenous ligand / Surfactant metabolism / collagen trimer / surfactant homeostasis / Signal regulatory protein family interactions / negative regulation of interleukin-2 production / lung alveolus development / macrophage chemotaxis / endocytic vesicle / negative regulation of T cell proliferation / positive regulation of phagocytosis / regulation of cytokine production / multivesicular body / reactive oxygen species metabolic process / extracellular matrix organization / receptor-mediated endocytosis / SARS-CoV-1 activates/modulates innate immune responses / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / collagen-containing extracellular matrix / lysosome / defense response to bacterium / innate immune response / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Shrive, A.K. / Greenhough, T.J. | ||||||
![]() | ![]() Title: Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325 Authors: Shrive, A.K. / Martin, C. / Burns, I. / Paterson, J.M. / Martin, J.D. / Townsend, J.P. / Waters, P. / Clark, H.W. / Kishore, U. / Reid, K.B.M. / Greenhough, T.J. #1: ![]() Title: High-resolution structural insights into ligand binding and immune cell recognition by human lung surfactant protein D. Authors: Shrive, A.K. / Tharia, H.A. / Strong, P. / Kishore, U. / Burns, I. / Rizkallah, P.J. / Reid, K.B.M. / Greenhough, T.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.1 KB | Display | ![]() |
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PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.1 KB | Display | ![]() |
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Full document | ![]() | 461.9 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ikpC ![]() 3ikqC ![]() 3ikrC ![]() 1pw9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18834.957 Da / Num. of mol.: 3 / Fragment: UNP residues 199-375 / Mutation: P180S Source method: isolated from a genetically manipulated source Details: recombinant trimeric fragment of alpha helical neck region plus carbohydrate recognition domain Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Sugar | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 4000, tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→55.9 Å / Num. obs: 83548 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 8.5 / Num. unique all: 10721 / Rsym value: 0.119 / % possible all: 84.6 |
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Processing
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Refinement | Method to determine structure: isomorphous to native crystals Starting model: 1pw9 Resolution: 1.6→55.86 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 44.287 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.7 Å2 / Biso mean: 23.323 Å2 / Biso min: 11.25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→55.86 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Xplor file |
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