6P3S | pdb_00006p3s

Crystal structure of human Fab H5.28 in complex with influenza A H5N1 Vietnam hemagglutinin head domain

PDB DOI: https://doi.org/10.2210/pdb6P3S/pdb

Classification: IMMUNE SYSTEM/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: 4.00 Å
R-Value Free:
0.326 (Depositor), 0.327 (DCC)
R-Value Work:
0.281 (Depositor), 0.284 (DCC)
R-Value Observed:
0.283 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

crystal structure of human Fab H5.28 in complex with influenza A H5N1 Vietnam hemagglutinin head domain

Dong, J., Crowe, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 596.23 kDa
Atom Count: 32,097
Modeled Residue Count: 4,991
Deposited Residue Count: 5,312
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Fab H5.28 heavy chain	A, C, F, I, M A, C, F, I, M, P, S, V	230	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Fab H5.28 light chain	B, D, G, J, N B, D, G, J, N, Q, T, W	215	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	E, H, K, L, O E, H, K, L, O, R, U, X	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1KHK2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E Focus chain H Focus chain K Focus chain O Focus chain R Focus chain U Focus chain X
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Y	7		N-Glycosylation	Interactions Focus chain Y Interactions & Density Focus chain Y
Glycosylation Resources
GlyTouCan: G59070FK GlyCosmos: G59070FK GlyGen: G59070FK

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Z	7		N-Glycosylation	Interactions Focus chain Z Interactions & Density Focus chain Z
Glycosylation Resources
GlyTouCan: G13564MD GlyCosmos: G13564MD GlyGen: G13564MD

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a]	6		N/A	Interactions Focus chain AA [auth a] Interactions & Density Focus chain AA [auth a]
Glycosylation Resources
GlyTouCan: G20631NH GlyCosmos: G20631NH GlyGen: G20631NH

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b]	7		N-Glycosylation	Interactions Focus chain BA [auth b] Interactions & Density Focus chain BA [auth b]
Glycosylation Resources
GlyTouCan: G87077ZT GlyCosmos: G87077ZT GlyGen: G87077ZT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	CA [auth c]	5		N/A	Interactions Focus chain CA [auth c] Interactions & Density Focus chain CA [auth c]
Glycosylation Resources
GlyTouCan: G19798XY GlyCosmos: G19798XY GlyGen: G19798XY

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d]	7		N/A	Interactions Focus chain DA [auth d] Interactions & Density Focus chain DA [auth d]
Glycosylation Resources
GlyTouCan: G77499AE GlyCosmos: G77499AE GlyGen: G77499AE

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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)-alpha-D-mannopyranose	EA [auth e]	5		N/A	Interactions Focus chain EA [auth e] Interactions & Density Focus chain EA [auth e]
Glycosylation Resources
GlyTouCan: G89628EO GlyCosmos: G89628EO GlyGen: G89628EO

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f]	7		N/A	Interactions Focus chain FA [auth f] Interactions & Density Focus chain FA [auth f]
Glycosylation Resources
GlyTouCan: G84134OD GlyCosmos: G84134OD GlyGen: G84134OD

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 KA [auth X] SDF format, chain JA [auth U] SDF format, chain IA [auth R] SDF format, chain HA [auth O] SDF format, chain GA [auth L] MOL2 format, chain KA [auth X] MOL2 format, chain JA [auth U] MOL2 format, chain IA [auth R] MOL2 format, chain HA [auth O] MOL2 format, chain GA [auth L] mmCIF format, chain KA [auth X] mmCIF format, chain JA [auth U] mmCIF format, chain IA [auth R] mmCIF format, chain HA [auth O] mmCIF format, chain GA [auth L]	GA [auth L], HA [auth O], IA [auth R], JA [auth U], KA [auth X]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain GA [auth L] Focus chain HA [auth O] Focus chain IA [auth R] Focus chain JA [auth U] Focus chain KA [auth X] Interactions & Density Focus chain GA [auth L] Focus chain HA [auth O] Focus chain IA [auth R] Focus chain JA [auth U] Focus chain KA [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.326 (Depositor), 0.327 (DCC)
R-Value Work: 0.281 (Depositor), 0.284 (DCC)
R-Value Observed: 0.283 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.48	α = 90
b = 187.225	β = 90
c = 342.366	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

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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, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

6P3S | pdb_00006p3s

Crystal structure of human Fab H5.28 in complex with influenza A H5N1 Vietnam hemagglutinin head domain

Literature

crystal structure of human Fab H5.28 in complex with influenza A H5N1 Vietnam hemagglutinin head domain

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Biological Assembly 7

Biological Assembly 8

Macromolecules

Entity ID: 1

Entity ID: 2

Entity ID: 3

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Oligosaccharides

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)