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.
Experimental Data Snapshot
Starting Models: experimental
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wwPDB Validation   3D Report Full Report
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Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Human Fab H5.28 heavy chain | 230 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Human Fab H5.28 light chain | 215 | Homo sapiens | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Hemagglutinin | 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 | |||||
Sequence AnnotationsExpand | |||||
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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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G59070FK GlyCosmos:  G59070FK GlyGen:  G59070FK |
Entity ID: 5 | |||||
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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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G13564MD GlyCosmos:  G13564MD GlyGen:  G13564MD |
Entity ID: 6 | |||||
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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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G20631NH GlyCosmos:  G20631NH GlyGen:  G20631NH |
Entity ID: 7 | |||||
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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 | ||
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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G19798XY GlyCosmos:  G19798XY GlyGen:  G19798XY |
Entity ID: 9 | |||||
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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 | ||
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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G89628EO GlyCosmos:  G89628EO GlyGen:  G89628EO |
Entity ID: 11 | |||||
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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 | ||
Glycosylation Resources | |||||
GlyTouCan:  G84134OD GlyCosmos:  G84134OD GlyGen:  G84134OD |
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | 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 |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 135.48 | α = 90 |
b = 187.225 | β = 90 |
c = 342.366 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
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Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | 5U19AI117905-05 |