6S08

Crystal Structure of Properdin (TSR domains N1 & 456)

• PDB DOI: https://doi.org/10.2210/pdb6S08/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-06-14 Released: 2019-09-04 
• Deposition Author(s): van den Bos, R.M., Pearce, N.M., Gros, P.
• Funding Organization(s): Dutch Kidney Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.248 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 39.05 kDa 
• Atom Count: 2,589 
• Modelled Residue Count: 311 
• Deposited Residue Count: 335 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Properdin	A	225	Homo sapiens	Mutation(s): 0  Gene Names: CFP, PFC
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens) Explore P27918  Go to UniProtKB:  P27918
PHAROS:  P27918 GTEx:  ENSG00000126759

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Properdin	B	110	Homo sapiens	Mutation(s): 0  Gene Names: CFP, PFC
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens) Explore P27918  Go to UniProtKB:  P27918
PHAROS:  P27918 GTEx:  ENSG00000126759

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G36855WW GlyCosmos:  G36855WW GlyGen:  G36855WW

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth A], M [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	N [auth B]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
PGE	J [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
NA	L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.248 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.995	α = 90
b = 114.86	β = 99.56
c = 39.822	γ = 90

Software Package:

Software Name	Purpose
DIALS	data reduction
STARANISO	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): van den Bos, R.M., Pearce, N.M., Gros, P.

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Funding Organization	Location	Grant Number
Dutch Kidney Foundation	Netherlands	13OCA27

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-10-02
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary