6XSD | pdb_00006xsd

Patient-derived B2GPI

• PDB DOI: https://doi.org/10.2210/pdb6XSD/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2020-07-15 Released: 2021-07-21 
• Deposition Author(s): Klenotic, P.A., Yu, E.W.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

B2-Glycoprotein I and it's role in APS

Klenotic, P.A., Yu, E.W.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.59 kDa 
• Atom Count: 2,625 
• Modeled Residue Count: 326 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-glycoprotein 1	A	326	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02749 (Homo sapiens) Explore P02749  Go to UniProtKB:  P02749
PHAROS:  P02749 GTEx:  ENSG00000091583
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P02749-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.463	α = 90
b = 167.566	β = 90
c = 114.161	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data scaling
PHENIX	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Klenotic, P.A., Yu, E.W.Y.

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary