4C55
Crystal structure of serum-derived human IgG4 Fc
- PDB DOI: https://doi.org/10.2210/pdb4C55/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Mutation(s): No 
- Deposited: 2013-09-10 Released: 2013-11-13 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.238 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
wwPDB Validation   3D Report Full Report
This is version 2.1 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-4 CHAIN C REGION | 218 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01861 (Homo sapiens) Explore P01861  Go to UniProtKB:  P01861 | |||||
PHAROS:  P01861 GTEx:  ENSG00000211892  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01861 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
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-(1-6)-[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 | 9 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G27919IH GlyCosmos:  G27919IH GlyGen:  G27919IH |
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-(1-6)-[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)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 8 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G89993FE GlyCosmos:  G89993FE GlyGen:  G89993FE |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
MES Query on MES | E [auth A], H [auth B] | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N | |||
EDO Query on EDO | F [auth A], G [auth A], I [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.238 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 74.298 | α = 90 |
b = 80.738 | β = 90 |
c = 99.19 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2013-11-13  Deposition Author(s): Davies, A.M., Rispens, T., Ooijevaar-deHeer, P., Gould, H.J., Jefferis, R., Aalberse, R.C., Sutton, B.J.
Revision History (Full details and data files)
- Version 1.0: 2013-11-13
Type: Initial release - Version 1.1: 2013-11-20
Changes: Database references - Version 1.2: 2014-02-05
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary