5WAV | pdb_00005wav

Fc AbVance: Increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery.

• PDB DOI: https://doi.org/10.2210/pdb5WAV/pdb

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


• Deposited: 2017-06-27 Released: 2017-11-08 
• Deposition Author(s): Williams, S.P., Reid, R.A., Convery, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.260 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

AbVance: Increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery.

Williams, S.P., Reid, R.A., Convery, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.77 kDa 
• Atom Count: 3,580 
• Modeled Residue Count: 414 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-1 heavy chain,Immunoglobulin gamma-1 heavy chain	A, B	220	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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, D	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G13625KU GlyCosmos: G13625KU GlyGen: G13625KU

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.260 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.532	α = 90
b = 79.977	β = 90
c = 139.658	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-08 
Deposition Author(s): Williams, S.P., Reid, R.A., Convery, M.A.

Revision History  

• Version 1.0: 2017-11-08
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary