6P3R

crystal structure of human Fab H5.31 in complex with influenza A H5N1 Vietnam hemagglutinin head domain

PDB DOI: https://doi.org/10.2210/pdb6P3R/pdb

Classification: VIRAL PROTEIN
Organism(s): Homo sapiens, Influenza A virus (A/chicken/Vietnam/32/2004(H5N1))
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2019-05-24 Released: 2020-05-27
Deposition Author(s): Dong, J., Crowe, J.E.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.226
R-Value Work: 0.192
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human Fab H5.31 in complex with influenza A H5N1 Vietnam hemagglutinin head domain

Dong, J., Crowe, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 150.94 kDa
Atom Count: 9,959
Modelled Residue Count: 1,294
Deposited Residue Count: 1,328
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
human Fab H5.31 heavy chain	A, C	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Fab H5.31 light chain	B, D	215	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	E, F [auth L]	219	Influenza A virus (A/chicken/Vietnam/32/2004(H5N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q1KHK2 (Influenza A virus) Explore Q1KHK2 Go to UniProtKB: Q1KHK2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1KHK2
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	G [auth F]	2		N-Glycosylation	Interactions Focus chain G [auth F] Interactions & Density Focus chain G [auth F]

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth G]	8		N/A	Interactions Focus chain H [auth G] Interactions & Density Focus chain H [auth G]

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fructofuranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth H]	8	N/A	N-Glycosylation	Interactions Focus chain I [auth H] Interactions & Density Focus chain I [auth H]

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 K [auth C] SDF format, chain M [auth E] SDF format, chain O [auth L] MOL2 format, chain K [auth C] MOL2 format, chain M [auth E] MOL2 format, chain O [auth L]	K [auth C], M [auth E], O [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth L] Interactions & Density Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth L]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth D] SDF format, chain N [auth L] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D] MOL2 format, chain N [auth L]	J [auth B], L [auth D], N [auth L]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth L] Interactions & Density Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.226
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.113	α = 90
b = 234.472	β = 90
c = 284.814	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-05-27

Deposition Author(s):

Dong, J.

Crowe, J.E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5U19AI117905-05

Revision History (Full details and data files)

Version 1.0: 2020-05-27
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary