3WN5
Crystal structure of asymmetrically engineered Fc variant in complex with FcgRIIIa
- PDB DOI: https://doi.org/10.2210/pdb3WN5/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2013-12-05 Released: 2014-11-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.78 Å
- R-Value Free: 0.274 
- R-Value Work: 0.236 
- R-Value Observed: 0.238 
This is version 2.0 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 | 230 | Homo sapiens | Mutation(s): 9  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 | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Ig gamma-1 chain C region | 230 | Homo sapiens | Mutation(s): 10  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 | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Low affinity immunoglobulin gamma Fc region receptor III-A | 197 | Homo sapiens | Mutation(s): 3  Gene Names: FCGR3A, CD16A, FCG3, FCGR3, IGFR3 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P08637 (Homo sapiens) Explore P08637  Go to UniProtKB:  P08637 | |||||
PHAROS:  P08637 GTEx:  ENSG00000203747  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P08637 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | G, H, L | 9 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G33244HE GlyCosmos:  G33244HE GlyGen:  G33244HE |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | I | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 6 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | J, M | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 7 | |||||
---|---|---|---|---|---|
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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | K | 8 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G59451NL GlyCosmos:  G59451NL GlyGen:  G59451NL |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | Z [auth F] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
IOD Query on IOD | AA [auth F] BA [auth F] CA [auth F] DA [auth F] N [auth A] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.78 Å
- R-Value Free: 0.274 
- R-Value Work: 0.236 
- R-Value Observed: 0.238 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 75.03 | α = 90 |
b = 72.49 | β = 91.15 |
c = 163.48 | γ = 90 |
Software Name | Purpose |
---|---|
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2014-11-19  Deposition Author(s): Kadono, S., Mimoto, F., Katada, H., Igawa, T., Kamikawa, T., Hattori, K.
Revision History (Full details and data files)
- Version 1.0: 2014-11-19
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary