4O5I
Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/361/2011 (H3N2) influenza hemagglutinin
- PDB DOI: https://doi.org/10.2210/pdb4O5I/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Influenza A virus (A/Singapore/H2011.447/2011(H3N2)), Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2013-12-19 Released: 2014-04-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 6.50 Å
- R-Value Free: 0.248 
- R-Value Work: 0.201 
- R-Value Observed: 0.203 
wwPDB Validation   3D Report Full Report
This is version 2.1 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 |
Hemagglutinin HA1 chain | 323 | Influenza A virus (A/Singapore/H2011.447/2011(H3N2)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for R9U684 (Influenza A virus) Explore R9U684  Go to UniProtKB:  R9U684 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | R9U684 | ||||
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 |
Hemagglutinin HA2 chain | 176 | Influenza A virus (A/Singapore/H2011.447/2011(H3N2)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for R9U684 (Influenza A virus) Explore R9U684  Go to UniProtKB:  R9U684 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | R9U684 | ||||
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 |
Fab F045-092 heavy chain | 240 | Homo sapiens | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for S6C4S0 (Homo sapiens) Explore S6C4S0  Go to UniProtKB:  S6C4S0 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | S6C4S0 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Fab F045-092 light chain | 216 | Homo sapiens | Mutation(s): 0  Gene Names: IGL@, IGLC2 | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 | AB [auth 0], DB [auth 3], FB [auth 5], GB [auth 6], IA [auth i], AB [auth 0], DB [auth 3], FB [auth 5], GB [auth 6], IA [auth i], JA [auth j], LA [auth l], PA [auth p], TA [auth t], UA [auth u], Y, YA [auth y], ZA [auth z] | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
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 | AA [auth a], BB [auth 1], CA [auth c], CB [auth 2], DA [auth d], AA [auth a], BB [auth 1], CA [auth c], CB [auth 2], DA [auth d], EB [auth 4], FA [auth f], OA [auth o], QA [auth q], RA [auth r], SA [auth s], VA [auth v], WA [auth w], XA [auth x], Z | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 7 | |||||
---|---|---|---|---|---|
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 | BA [auth b], HA [auth h], KA [auth k], NA [auth n] | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 8 | |||||
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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)-2-acetamido-2-deoxy-beta-D-glucopyranose | EA [auth e], GA [auth g], MA [auth m] | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | HB [auth B] IB [auth C] JB [auth D] KB [auth E] LB [auth F] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 6.50 Å
- R-Value Free: 0.248 
- R-Value Work: 0.201 
- R-Value Observed: 0.203 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 318.123 | α = 90 |
b = 187.167 | β = 90.47 |
c = 353.636 | γ = 90 |
Software Name | Purpose |
---|---|
Blu-Ice | data collection |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
Entry History 
Deposition Data
- Released Date: 2014-04-16  Deposition Author(s): Lee, P.S., Wilson, I.A.
Revision History (Full details and data files)
- Version 1.0: 2014-04-16
Type: Initial release - Version 1.1: 2014-05-14
Changes: Database references - Version 1.2: 2017-08-02
Changes: Refinement description, Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2024-04-03
Changes: Data collection, Database references, Refinement description, Structure summary