6CMG
Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent Cross-Reactive Neutralizing Human Monoclonal Antibody m102.3
- PDB DOI: https://doi.org/10.2210/pdb6CMG/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Hendra virus horse/Australia/Hendra/1994, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2018-03-05 Released: 2018-04-18 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.275 
- R-Value Work: 0.229 
- R-Value Observed: 0.232 
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 |
Glycoprotein G | 428 | Hendra virus horse/Australia/Hendra/1994 | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for O89343 (Hendra virus (isolate Horse/Autralia/Hendra/1994)) Explore O89343  Go to UniProtKB:  O89343 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O89343 | ||||
Sequence AnnotationsExpand | |||||
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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
m102.3 light chain | 214 | 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: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
IgG Heavy chain | 235 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, E, F | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | G | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G17601US GlyCosmos:  G17601US GlyGen:  G17601US |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.275 
- R-Value Work: 0.229 
- R-Value Observed: 0.232 
- Space Group: P 61 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 72.916 | α = 90 |
b = 72.916 | β = 90 |
c = 653.814 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-04-18  Deposition Author(s): Xu, K., Nikolov, D.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI054715 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI077995 |
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) | United States | NS38586 |
Revision History (Full details and data files)
- Version 1.0: 2018-04-18
Type: Initial release - Version 1.1: 2018-04-25
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2019-02-20
Changes: Author supporting evidence, Data collection - Version 1.3: 2019-12-18
Changes: Author supporting evidence, Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary