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
Deposition Author(s): Whittle, J.R.R., Jenni, S., Harrison, S.C.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 313.21 kDa
Atom Count: 21,882
Modelled Residue Count: 2,781
Deposited Residue Count: 2,799
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E	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 Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F	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 Annotations Expand
Reference Sequence

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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 Annotations Expand
Reference Sequence

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(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 Annotations Expand
Reference Sequence

Oligosaccharides

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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	Interactions Focus chain M [auth G] Focus chain O Focus chain P Focus chain R Focus chain S Focus chain U Interactions & Density Focus chain M [auth G] Focus chain O Focus chain P Focus chain R Focus chain S Focus chain U
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	Interactions Focus chain N [auth K] Focus chain Q Focus chain T Interactions & Density Focus chain N [auth K] Focus chain Q Focus chain T
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 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth E]	AA [auth E] V [auth A] W [auth A] X [auth C] Y [auth C] AA [auth E], V [auth A], W [auth A], X [auth C], Y [auth C], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth E] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth E]

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 Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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