5OXR

Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R7 oligosaccharide

• PDB DOI: https://doi.org/10.2210/pdb5OXR/pdb

• Classification: SURFACTANT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-07 Released: 2018-06-20 
• Deposition Author(s): Shrive, A.K., Greenhough, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.196 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.07 kDa 
• Atom Count: 4,053 
• Modelled Residue Count: 454 
• Deposited Residue Count: 531 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pulmonary surfactant-associated protein D	A, B, C	177	Homo sapiens	Mutation(s): 0  Gene Names: SFTPD, COLEC7, PSPD, SFTP4
UniProt & NIH Common Fund Data Resources
Find proteins for P35247 (Homo sapiens) Explore P35247  Go to UniProtKB:  P35247
PHAROS:  P35247 GTEx:  ENSG00000133661

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-4,7-anhydro-3-deoxy-D-gluco-oct-2-ulosonic acid	D, E	3		N/A
Glycosylation Resources
GlyTouCan:  G37225SX GlyCosmos:  G37225SX

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.196 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.329	α = 90
b = 108.14	β = 91.82
c = 55.67	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Shrive, A.K., Greenhough, T.J.

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2018-06-27
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary