3G83

Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with alpha 1,2 dimannose.

• PDB DOI: https://doi.org/10.2210/pdb3G83/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-11 Released: 2009-03-17 
• Deposition Author(s): Head, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.215 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

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)

Macromolecule Content

• Total Structure Weight: 53.2 kDa 
• Atom Count: 4,089 
• Modelled Residue Count: 452 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pulmonary surfactant-associated protein D	A, B, C	160	Homo sapiens	Mutation(s): 0  Gene Names: SFTPD, 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
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	D, E, F	2		N/A
Glycosylation Resources
GlyTouCan:  G53402KW GlyCosmos:  G53402KW GlyGen:  G53402KW

Small Molecules

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111	D, E, F	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.215 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.754	α = 90
b = 108.774	β = 91.58
c = 56.011	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Head, J.F.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary