5A3I

Crystal Structure of a Complex formed between FLD194 Fab and Transmissible Mutant H5 Haemagglutinin

PDB DOI: https://doi.org/10.2210/pdb5A3I/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1)), Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2015-06-01 Released: 2015-07-22
Deposition Author(s): Xiong, X., Corti, D., Liu, J., Pinna, D., Foglierini, M., Calder, L.J., Martin, S.R., Lin, Y.P., Walker, P.A., Collins, P.J., Monne, I., Suguitan Jr, A.L., Santos, C., Temperton, N.J., Subbarao, K., Lanzavecchia, A., Gamblin, S.J., Skehel, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.277
R-Value Work: 0.244
R-Value Observed: 0.245

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: 210.51 kDa
Atom Count: 14,561
Modelled Residue Count: 1,866
Deposited Residue Count: 1,886
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ	A, E	328	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33 Go to UniProtKB: Q6DQ33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6DQ33
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ	B	166	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0
UniProt
Find proteins for A8UDR1 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore A8UDR1 Go to UniProtKB: A8UDR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8UDR1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTI-HAEMAGGLUTININ HA1 FAB HEAVY CHAIN	C, G	230	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTI-HAEMAGGLUTININ HA1 FAB LIGHT CHAIN	D, H	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMAGGLUTININ	F	166	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0
UniProt
Find proteins for A8UDR1 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore A8UDR1 Go to UniProtKB: A8UDR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8UDR1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	I, J	2		N-Glycosylation	Interactions Focus chain I Focus chain J Interactions & Density Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 K [auth E] MOL2 format, chain K [auth E]	K [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth E] Interactions & Density Focus chain K [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.277
R-Value Work: 0.244
R-Value Observed: 0.245
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.75	α = 78.67
b = 87.7	β = 84.66
c = 100.9	γ = 73.91

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-07-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-22
Type: Initial release
Version 1.1: 2015-08-12
Changes: Database references
Version 1.2: 2015-09-09
Changes: Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary