6E4X
Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2)
- PDB DOI: https://doi.org/10.2210/pdb6E4X/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Influenza A virus (A/Texas/50/2012(H3N2)), Homo sapiens
- Expression System: Trichoplusia ni, Homo sapiens
- Mutation(s): No
- Deposited: 2018-07-18 Released: 2019-05-22
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.225
- R-Value Work: 0.203
- R-Value Observed: 0.204
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 |
| Hemagglutinin | A [auth B] | 291 | Influenza A virus (A/Texas/50/2012(H3N2)) | Mutation(s): 0 Gene Names: HA, L998_47834gpHA |  |
UniProt | |||||
Find proteins for R4L1D1 (Influenza A virus) Explore R4L1D1 Go to UniProtKB: R4L1D1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | R4L1D1 | ||||
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 |
| S5V2-29 light chain | B [auth Y] | 210 | Homo sapiens | Mutation(s): 0 Gene Names: IGKV1-39*01 |  |
UniProt | |||||
Find proteins for Q8TCD0 (Homo sapiens) Explore Q8TCD0 Go to UniProtKB: Q8TCD0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8TCD0 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| S5V2-29 heavy chain | C [auth Z] | 241 | Homo sapiens | Mutation(s): 0 Gene Names: IGHV4-61*01 |  |
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 |
| 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 | D [auth A] | 5 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF | |||||
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E [auth C] | 3 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | F [auth D] | 4 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G18638YB GlyCosmos: G18638YB GlyGen: G18638YB | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | G [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| GOL Query on GOL | H [auth B], I [auth B], J [auth B], K [auth Y] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.25 Å
- R-Value Free: 0.225
- R-Value Work: 0.203
- R-Value Observed: 0.204
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 115.74 | α = 90 |
| b = 163.48 | β = 90 |
| c = 136.37 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-05-22 Deposition Author(s): McCarthy, K.R., Harrison, S.C.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | P01AI089618 |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | 1U19AI117892-01 |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI128832 |
Revision History (Full details and data files)
- Version 1.0: 2019-05-22
Type: Initial release - Version 1.1: 2019-05-29
Changes: Data collection, Database references - Version 1.2: 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
