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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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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(by identity cutoff) | 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% 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

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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-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	3D 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	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-(1-4)-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	3D 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	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	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	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)-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	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)-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	3D 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

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