2VDQ

Integrin AlphaIIbBeta3 Headpiece Bound to a Chimeric Fibrinogen Gamma chain peptide, HHLGGAKQRGDV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INTEGRIN ALPHA-IIB452Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08514 (Homo sapiens)
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Go to UniProtKB:  P08514
PHAROS:  P08514
GTEx:  ENSG00000005961 
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UniProt GroupP08514
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
INTEGRIN BETA-3461Homo sapiensMutation(s): 0 
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Find proteins for P05106 (Homo sapiens)
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Go to UniProtKB:  P05106
PHAROS:  P05106
GTEx:  ENSG00000259207 
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UniProt GroupP05106
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FIBRINOGEN, GAMMA POLYPEPTIDE12Homo sapiensMutation(s): 1 
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Find proteins for P02679 (Homo sapiens)
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Go to UniProtKB:  P02679
PHAROS:  P02679
GTEx:  ENSG00000171557 
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UniProt GroupP02679
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MONOCLONAL ANTIBODY 10E5 HEAVY CHAIND [auth H]221Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
MONOCLONAL ANTIBODY 10E5 LIGHT CHAINE [auth L]214Mus musculusMutation(s): 0 
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Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[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-glucopyranoseF [auth D]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21381MC
GlyCosmos:  G21381MC
GlyGen:  G21381MC
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09609EN
GlyCosmos:  G09609EN
GlyGen:  G09609EN
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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M [auth A],
N [auth A],
S [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

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H [auth A],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

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I [auth A]
J [auth A]
K [auth A]
L [auth A]
Q [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
Q [auth B],
R [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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P [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.331α = 90
b = 148.331β = 90
c = 176.567γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-11-20
    Changes: Advisory, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary