4JTV

Crystal structure of 2009 pandemic influenza virus hemagglutinin complexed with human receptor analogue LSTc

PDB DOI: https://doi.org/10.2210/pdb4JTV/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/California/04/2009(H1N1))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2013-03-24 Released: 2013-05-01
Deposition Author(s): Zhang, W., Shi, Y., Qi, J., Gao, F., Li, Q., Fan, Z., Yan, J., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.275
R-Value Work: 0.224
R-Value Observed: 0.226

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: 331.66 kDa
Atom Count: 23,528
Modelled Residue Count: 2,896
Deposited Residue Count: 2,898
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E, G, I A, C, E, G, I, K	321	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S1 Go to UniProtKB: C3W5S1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3W5S1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F, H, J B, D, F, H, J, L	162	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S1 Go to UniProtKB: C3W5S1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3W5S1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, Q, R	3		N/A	Interactions Focus chain M Focus chain Q Focus chain R Interactions & Density Focus chain M Focus chain Q Focus chain R
Glycosylation Resources
GlyTouCan: G73578JC GlyCosmos: G73578JC GlyGen: G73578JC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	N, P	4		N/A	Interactions Focus chain N Focus chain P Interactions & Density Focus chain N Focus chain P
Glycosylation Resources
GlyTouCan: G03509EL GlyCosmos: G03509EL GlyGen: G03509EL

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	O	2		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain Z [auth G] MOL2 format, chain Z [auth G]	Z [auth G]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain Z [auth G] Interactions & Density Focus chain Z [auth G]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth C] SDF format, chain X [auth G] SDF format, chain Y [auth G] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth C] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G]	S [auth A] T [auth A] U [auth A] V [auth A] W [auth C] S [auth A], T [auth A], U [auth A], V [auth A], W [auth C], X [auth G], Y [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth C] Focus chain X [auth G] Focus chain Y [auth G] Interactions & Density Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth C] Focus chain X [auth G] Focus chain Y [auth G]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046 Query on PRD_900046	M, Q, R	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component		Interactions Focus chain M Focus chain Q Focus chain R Interactions & Density Focus chain M Focus chain Q Focus chain R

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.275
R-Value Work: 0.224
R-Value Observed: 0.226
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.722	α = 61.78
b = 117.321	β = 81.82
c = 117.393	γ = 77.42

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-05-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-01
Type: Initial release
Version 1.1: 2013-08-07
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary