7KG4 | pdb_00007kg4

Recombinant Beta-2-Glycoprotein I antibody recognition loop mutant

• PDB DOI: https://doi.org/10.2210/pdb7KG4/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2020-10-15 Released: 2021-10-20 
• Deposition Author(s): Klenotic, P.A., Yu, E.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.298 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.283 (Depositor), 0.285 (DCC) 
• R-Value Observed: 
  0.284 (Depositor) 

Starting Model: experimental

Literature

Beta-2-Glycoprotein I and its role in APS

Klenotic, P.A., Yu, E.W.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.46 kDa 
• Atom Count: 5,268 
• Modeled Residue Count: 652 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-glycoprotein 1	A, B	326	Homo sapiens	Mutation(s): 4  Gene Names: APOH, B2G1
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: 3		Go to GlyGen: P02749-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G47477HI GlyCosmos: G47477HI GlyGen: G47477HI

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	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	G [auth A], H [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.298 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.283 (Depositor), 0.285 (DCC) 
• R-Value Observed: 0.284 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.209	α = 90
b = 114.694	β = 96.92
c = 124.293	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-10-20 
Deposition Author(s): Klenotic, P.A., Yu, E.W.

Revision History  

• Version 1.0: 2021-10-20
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary