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

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 2.2 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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Fab H5.31 light chain	B, D	215	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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(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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E Focus chain F [auth L]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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] mmCIF format, chain K [auth C] mmCIF format, chain M [auth E] mmCIF 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] mmCIF format, chain J [auth B] mmCIF format, chain L [auth D] mmCIF 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
Version 2.2: 2024-10-23
Changes: Structure summary