1HEZ

Structure of P. magnus protein L bound to a human IgM Fab.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Complex between Peptostreptococcus Magnus Protein L and a Human Antibody Reveals Structural Convergence in the Interaction Modes of Fab Binding Modes

Graille, M.Stura, E.A.Housden, N.G.Beckingham, J.A.Bottomley, S.P.Beale, D.Taussig, M.J.Sutton, B.J.Gore, M.G.Charbonnier, J.B.

(2001) Structure 9: 679

  • DOI: 10.1016/s0969-2126(01)00630-x
  • Primary Citation of Related Structures:  
    1HEZ

  • PubMed Abstract: 
  • Peptostreptococcus magnus protein L (PpL) is a multidomain, bacterial surface protein whose presence correlates with virulence. It consists of up to five homologous immunoglobulin binding domains that interact with the variable (VL) regions of kappa light chains found on two thirds of mammalian antibodies ...

    Peptostreptococcus magnus protein L (PpL) is a multidomain, bacterial surface protein whose presence correlates with virulence. It consists of up to five homologous immunoglobulin binding domains that interact with the variable (VL) regions of kappa light chains found on two thirds of mammalian antibodies.


    Related Citations: 
    • Interactions between a Single Immunoglobulin-Binding Domain of Protein L from Peptostreptococcus Magnus and a Human Kappa Light Chain
      Beckingham, J.A., Bottomley, S.P., Hinton, R., Sutton, B.J., Gore, M.G.
      (1999) Biochem J 340: 193
    • Crystal Structure of a Staphylococcus Aureus Protein a Domain Complexed with the Fab Fragment of a Human Igm Antibody: Structural Basis for Recognition of B-Cell Receptors and Superantigen Activity
      Graille, M., Stura, E.A., Corper, A.L., Sutton, B.J., Taussig, M.J., Charbonnier, J.B., Silverman, G.J.
      (2000) Proc Natl Acad Sci U S A 97: 5399
    • Cloning, expression and purification of Ppl-1, a kappa-chain binding protein, based upon protein L from Peptostreptococcus magnus.
      Bottomley, S.P., Beckingham, J.A., Murphy, J.P., Atkinson, M., Atkinson, T., Hinton, R.J., Gore, M.G.
      (1995) Bioseparation 5: 359

    Organizational Affiliation

    Département d'Ingénierie et d'Etudes des Protéines, Commissariat à l'Energie Atomique, Centre d'Etudes Saclay, F-91191, Gif-sur-Yvette, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KAPPA LIGHT CHAIN OF IGA, C214Homo sapiensMutation(s): 0 
Gene Names: IGKC
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
PHAROS:  P01834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01834
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HEAVY CHAIN OF IGB, D224Homo sapiensMutation(s): 0 
Gene Names: IGHM
UniProt & NIH Common Fund Data Resources
Find proteins for P01871 (Homo sapiens)
Explore P01871 
Go to UniProtKB:  P01871
PHAROS:  P01871
Entity Groups  
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UniProt GroupP01871
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN LE61Finegoldia magnaMutation(s): 0 
UniProt
Find proteins for Q51918 (Finegoldia magna)
Explore Q51918 
Go to UniProtKB:  Q51918
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51918
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth C]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.185α = 90
b = 87.335β = 90
c = 210.538γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKLdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2021-03-17
    Changes: Derived calculations, Other, Structure summary