4BYH
Crystal structure of sialylated IgG Fc
- PDB DOI: https://doi.org/10.2210/pdb4BYH/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2013-07-19 Released: 2013-08-21 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.262 
- R-Value Work: 0.222 
- R-Value Observed: 0.224 
wwPDB Validation   3D Report Full Report
This is version 3.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
IG GAMMA-1 CHAIN C REGION | 233 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857 | |||||
PHAROS:  P01857 GTEx:  ENSG00000211896  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01857 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-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 | 10 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G23295TF GlyCosmos:  G23295TF GlyGen:  G23295TF |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-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 | D | 10 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G78059CC GlyCosmos:  G78059CC GlyGen:  G78059CC |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CL Query on CL | E [auth A], F [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.262 
- R-Value Work: 0.222 
- R-Value Observed: 0.224 
- Space Group: P 61 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 153 | α = 90 |
b = 153 | β = 90 |
c = 111.85 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
xia2 | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2013-08-21  Deposition Author(s): Crispin, M., Yu, X., Bowden, T.A.
Revision History (Full details and data files)
- Version 1.0: 2013-08-21
Type: Initial release - Version 1.1: 2013-10-02
Changes: Database references - Version 1.2: 2018-02-28
Changes: Source and taxonomy - Version 1.3: 2019-04-03
Changes: Data collection, Derived calculations, Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 3.0: 2020-12-23
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2023-12-20
Changes: Data collection, Database references, Refinement description