4I7J

T4 Lysozyme L99A/M102H with benzene bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition.

Merski, M.Shoichet, B.K.

(2013) J Med Chem 56: 2874-2884

  • DOI: 10.1021/jm301823g
  • Primary Citation of Related Structures:  
    4I7J, 4I7K, 4I7L, 4I7M, 4I7N, 4I7O, 4I7P, 4I7Q, 4I7R, 4I7S, 4I7T

  • PubMed Abstract: 
  • Simplified model binding sites allow one to isolate entangled terms in molecular energy functions. Here, we investigate the effects on ligand recognition of the introduction of a histidine into a hydrophobic cavity in lysozyme. We docked 656040 molecules and tested 26 highly and nine poorly ranked ...

    Simplified model binding sites allow one to isolate entangled terms in molecular energy functions. Here, we investigate the effects on ligand recognition of the introduction of a histidine into a hydrophobic cavity in lysozyme. We docked 656040 molecules and tested 26 highly and nine poorly ranked. Twenty-one highly ranked molecules bound and five were false positives, while three poorly ranked molecules were false negatives. In the 16 X-ray complexes now known, the docking predictions overlaid well with the crystallographic results. Although ligand enrichment was high, the false negatives, the false positives, and the inability to rank order illuminated weaknesses in our scoring, particularly overweighed apolar and underweighted polar terms. Adjusting these led to new problems, reflecting the entangled nature of docking scoring functions. Changes in ligand affinity relative to other lysozyme cavities speak to the subtleties of molecular recognition even in these simple sites and to their relevance for testing different models of recognition.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 Fourth Street, San Francisco, California 94158-2550, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LysozymeA, B187Escherichia virus T4Mutation(s): 8 
Gene Names: E
EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HED (Subject of Investigation/LOI)
Query on HED

Download Ideal Coordinates CCD File 
L [auth A]2-HYDROXYETHYL DISULFIDE
C4 H10 O2 S2
KYNFOMQIXZUKRK-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], O [auth B], P [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
C [auth A], I [auth A], J [auth A], K [auth A], M [auth B], R [auth B], S [auth B]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
BNZ
Query on BNZ

Download Ideal Coordinates CCD File 
D [auth A], N [auth B]BENZENE
C6 H6
UHOVQNZJYSORNB-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A], Q [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BNZ Binding MOAD:  4I7J Kd: 4.80e+5 (nM) from 1 assay(s)
PDBBind:  4I7J Kd: 4.80e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.39α = 90
b = 75.58β = 93.28
c = 52.6γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-24
    Changes: Database references