4GMS

Crystal structure of heterosubtypic Fab S139/1 in complex with influenza A H3 hemagglutinin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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This is version 3.1 of the entry. See complete history. 



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E
320Influenza A virus (A/Victoria/3/1975(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P03435 (Influenza A virus (strain A/Victoria/3/1975 H3N2))
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Go to UniProtKB:  P03435
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03435
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F
176Influenza A virus (A/Victoria/3/1975(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for P03435 (Influenza A virus (strain A/Victoria/3/1975 H3N2))
Explore P03435 
Go to UniProtKB:  P03435
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03435
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab S139/1 light chainG [auth L],
I [auth M],
K [auth N]		214Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab S139/1 heavy chainH,
J [auth I],
L [auth J]		225Mus musculusMutation(s): 0 
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Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth G],
O,
P,
U,
X		2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[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-glucopyranoseN [auth K],
Q,
V		5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
R, T
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
S, W
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
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AB [auth J]
FA [auth B]
KA [auth C]
LA [auth C]
PA [auth D]
AB [auth J],
FA [auth B],
KA [auth C],
LA [auth C],
PA [auth D],
VA [auth F],
Y [auth A],
YA [auth I],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4
Query on PG4
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UA [auth E]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4
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AA [auth A]
BA [auth A]
BB [auth J]
CA [auth A]
DA [auth A]
AA [auth A],
BA [auth A],
BB [auth J],
CA [auth A],
DA [auth A],
EA [auth A],
GA [auth B],
HA [auth B],
IA [auth B],
MA [auth C],
NA [auth C],
OA [auth C],
QA [auth D],
RA [auth D],
TA [auth E],
WA [auth F],
XA [auth H],
ZA [auth I]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL
Download Ideal Coordinates CCD File 
JA [auth B],
SA [auth D]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA		H,
J [auth I],
L [auth J]		L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.51α = 90
b = 112.94β = 118.76
c = 196.97γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2012-10-31
    Changes: Database references
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary