5D6C

Structure of 4497 Fab bound to synthetic wall teichoic acid fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Novel antibody-antibiotic conjugate eliminates intracellular S. aureus.

Lehar, S.M.Pillow, T.Xu, M.Staben, L.Kajihara, K.K.Vandlen, R.DePalatis, L.Raab, H.Hazenbos, W.L.Morisaki, J.H.Kim, J.Park, S.Darwish, M.Lee, B.C.Hernandez, H.Loyet, K.M.Lupardus, P.Fong, R.Yan, D.Chalouni, C.Luis, E.Khalfin, Y.Plise, E.Cheong, J.Lyssikatos, J.P.Strandh, M.Koefoed, K.Andersen, P.S.Flygare, J.A.Wah Tan, M.Brown, E.J.Mariathasan, S.

(2015) Nature 527: 323-328

  • DOI: https://doi.org/10.1038/nature16057
  • Primary Citation of Related Structures:  
    5D6C

  • PubMed Abstract: 

    Staphylococcus aureus is considered to be an extracellular pathogen. However, survival of S. aureus within host cells may provide a reservoir relatively protected from antibiotics, thus enabling long-term colonization of the host and explaining clinical failures and relapses after antibiotic therapy. Here we confirm that intracellular reservoirs of S. aureus in mice comprise a virulent subset of bacteria that can establish infection even in the presence of vancomycin, and we introduce a novel therapeutic that effectively kills intracellular S. aureus. This antibody-antibiotic conjugate consists of an anti-S. aureus antibody conjugated to a highly efficacious antibiotic that is activated only after it is released in the proteolytic environment of the phagolysosome. The antibody-antibiotic conjugate is superior to vancomycin for treatment of bacteraemia and provides direct evidence that intracellular S. aureus represents an important component of invasive infections.


  • Organizational Affiliation

    Infectious Diseases Department, Genentech Inc., South San Francisco, California 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4497 antibody IgK (VL and CL)A,
D [auth L]
220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
4497 antibody IgG1 (VH and CH1)B,
C [auth H]
224Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
57S
Query on 57S

Download Ideal Coordinates CCD File 
G [auth B],
M [auth L]
4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-5-O-phosphono-D-ribitol
C13 H26 N O13 P
VRKCYAMLHZHZPR-BXGOZMQFSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth H]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth H],
L
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H,
K [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.707α = 90
b = 111.471β = 90
c = 158.412γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Database references, Derived calculations, Structure summary