6N9T
Structure of a peptide-based photo-affinity cross-linker with Herceptin Fc
- PDB DOI: https://doi.org/10.2210/pdb6N9T/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2018-12-04 Released: 2019-01-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.58 Å
- R-Value Free: 0.265 
- R-Value Work: 0.229 
- R-Value Observed: 0.231 
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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Immunoglobulin G1 FC | A, C [auth B] | 224 | Homo sapiens | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q6MZV7 (Homo sapiens) Explore Q6MZV7  Go to UniProtKB:  Q6MZV7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6MZV7 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Photo-affinity peptide | B [auth E], D [auth F] | 13 | synthetic construct | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | E [auth C] | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G20449BJ GlyCosmos:  G20449BJ GlyGen:  G20449BJ |
Entity ID: 4 | |||||
---|---|---|---|---|---|
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 | F [auth D] | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G45889JQ GlyCosmos:  G45889JQ GlyGen:  G45889JQ |
Small Molecules
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
PBF Query on PBF | B [auth E], D [auth F] | L-PEPTIDE LINKING | C16 H15 N O3 | PHE |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.58 Å
- R-Value Free: 0.265 
- R-Value Work: 0.229 
- R-Value Observed: 0.231 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 66.112 | α = 90 |
b = 60.85 | β = 103.13 |
c = 68.167 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2019-01-16  Deposition Author(s): Sadowsky, J., Ultsch, M., Vance, N., Wang, W.
Revision History (Full details and data files)
- Version 1.0: 2019-01-16
Type: Initial release - Version 1.1: 2019-05-01
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary