3D6G
Fc fragment of IgG1 (Herceptin) with protein-A mimetic peptide dendrimer ligand.
- PDB DOI: https://doi.org/10.2210/pdb3D6G/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No 
- Deposited: 2008-05-19 Released: 2009-06-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.257 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Ig gamma-1 chain C region | 210 | Homo sapiens | Mutation(s): 0  Gene Names: IGHG1 | ||
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 |
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)]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, D | 8 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G80858MF GlyCosmos:  G80858MF GlyGen:  G80858MF |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
X12 Query on X12 | E [auth B] | 2-[[(2S)-2,6-bis[[(2S)-2,6-bis[[(2R)-2-[[(2R,3R)-2-[[(2R)-2-amino-5-carbamimidamido-pentanoyl]amino]-3-hydroxy-butanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]hexanoyl]amino]hexanoyl]amino]ethanoic acid C96 H153 N31 O25 GFRBISAVUSZQEP-GABXEQJVSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.257 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 49.778 | α = 90 |
b = 79.155 | β = 90 |
c = 139.223 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2009-06-16  Deposition Author(s): Bujacz, A.D., Redzynia, I., Bujacz, G.D., Dinon, F., Pengo, P., Fassina, G.
Revision History (Full details and data files)
- Version 1.0: 2009-06-16
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2019-12-25
Changes: Data collection, Database references, Derived calculations - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary