5UGY
Influenza hemagglutinin in complex with a neutralizing antibody
- PDB DOI: https://doi.org/10.2210/pdb5UGY/pdb
- Entry: 5UGY supersedes: 3SM5
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Influenza A virus (A/Solomon Islands/3/2006(H1N1)), Homo sapiens
- Expression System: Trichoplusia ni, Homo sapiens
- Mutation(s): No 
- Deposited: 2017-01-10 Released: 2017-01-25 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.289 
- R-Value Work: 0.259 
- R-Value Observed: 0.260 
This is version 2.1 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 HA1 | 323 | Influenza A virus (A/Solomon Islands/3/2006(H1N1)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for A7Y8A6 (Influenza A virus) Explore A7Y8A6  Go to UniProtKB:  A7Y8A6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A7Y8A6 | ||||
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 | 173 | Influenza A virus (A/Solomon Islands/3/2006(H1N1)) | Mutation(s): 0  Gene Names: HA | ||
UniProt | |||||
Find proteins for A7Y8I1 (Influenza A virus) Explore A7Y8I1  Go to UniProtKB:  A7Y8I1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A7Y8I1 | ||||
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 |
CH65 heavy chain | G [auth H], H [auth I], I [auth J] | 227 | 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 |
CH65 light chain | J [auth L], K [auth M], L [auth N] | 210 | Homo sapiens | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q8N355 (Homo sapiens) Explore Q8N355  Go to UniProtKB:  Q8N355 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q8N355 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | M [auth G], O, P, R, S, M [auth G], O, P, R, S, U | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
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)-2-acetamido-2-deoxy-beta-D-glucopyranose | N [auth K], Q, T | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth E] V [auth A] W [auth A] X [auth C] Y [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.289 
- R-Value Work: 0.259 
- R-Value Observed: 0.260 
- Space Group: I 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 154.824 | α = 90 |
b = 192.19 | β = 90 |
c = 333.219 | γ = 90 |
Software Name | Purpose |
---|---|
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2017-01-25  Deposition Author(s): Whittle, J.R.R., Jenni, S., Harrison, S.C.
- This entry supersedes: 3SM5
Revision History (Full details and data files)
- Version 1.0: 2017-01-25
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary