5W08

A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab

PDB DOI: https://doi.org/10.2210/pdb5W08/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: 2017-05-30 Released: 2018-02-14
Deposition Author(s): McCarthy, K.R., Harrison, S.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.262
R-Value Work: 0.240
R-Value Observed: 0.241

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: 498.03 kDa
Atom Count: 34,382
Modelled Residue Count: 4,324
Deposited Residue Count: 4,494
Unique protein chains: 3

Macromolecules

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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
K03.12 antibody heavy chain	G, I, K, M, O G, I, K, M, O, Q	244	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
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
K03.12 antibody light chain	H, J, L, N, P H, J, L, N, P, R	214	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6IPQ0 (Homo sapiens) Explore Q6IPQ0 Go to UniProtKB: Q6IPQ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6IPQ0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	S, V, W, Y, Z	2		N-Glycosylation	Interactions Focus chain S Focus chain V Focus chain W Focus chain Y Focus chain Z Interactions & Density Focus chain S Focus chain V Focus chain W Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	AA [auth a], BA [auth b], T, U, X	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain T Focus chain U Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain T Focus chain U Focus chain X
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain RA [auth F] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth B] SDF format, chain IA [auth C] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain PA [auth F] SDF format, chain QA [auth F] MOL2 format, chain CA [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain RA [auth F] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F]	CA [auth A] DA [auth A] EA [auth A] FA [auth B] GA [auth C] CA [auth A], DA [auth A], EA [auth A], FA [auth B], GA [auth C], HA [auth C], IA [auth C], JA [auth D], KA [auth D], LA [auth D], MA [auth E], NA [auth E], OA [auth E], PA [auth F], QA [auth F], RA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain SA [auth I] MOL2 format, chain SA [auth I]	SA [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain SA [auth I] Interactions & Density Focus chain SA [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.262
R-Value Work: 0.240
R-Value Observed: 0.241
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.8	α = 90
b = 325.12	β = 97.63
c = 156.99	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-14

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

Revision History (Full details and data files)

Version 1.0: 2018-02-14
Type: Initial release
Version 1.1: 2019-12-11
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

5W08

A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

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Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)