6GFE
High-resolution Structure of a therapeutic full-length anti-NPRA Antibody with exceptional Conformational Diversity
- PDB DOI: https://doi.org/10.2210/pdb6GFE/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No 
- Deposited: 2018-04-30 Released: 2019-05-15 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.200 
- R-Value Work: 0.181 
- R-Value Observed: 0.182 
wwPDB Validation   3D Report Full Report
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 |
Immunoglobulin gamma-4 heavy chain | A [auth H], B [auth K] | 450 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Immunoglobulin gamma-4 light chain | C [auth L], D [auth M] | 215 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 | E [auth A], F [auth B] | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G45889JQ GlyCosmos:  G45889JQ GlyGen:  G45889JQ |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
ACT Query on ACT | I [auth K], J [auth L], K [auth L] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M | |||
CA Query on CA | G [auth H], H [auth K] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.200 
- R-Value Work: 0.181 
- R-Value Observed: 0.182 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 65.78 | α = 90 |
b = 160.51 | β = 110.72 |
c = 87.3 | γ = 90 |
Software Name | Purpose |
---|---|
XDS | data reduction |
SCALA | data scaling |
BUSTER | refinement |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2019-05-15  Deposition Author(s): Hoerer, S.
Revision History (Full details and data files)
- Version 1.0: 2019-05-15
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary