5HNM

Crystal structure of vancomycin resistance D,D-pentapeptidase VanY E175A mutant from VanB-type resistance cassette in complex with Zn(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

To be published

Stogios, P.J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-alanyl-D-alanine carboxypeptidase
A, B, C, D, E, F
197Enterococcus faecalis (strain ATCC 700802 / V583)Mutation(s): 1 
Gene Names: vanYB
EC: 3.4.16.4
Find proteins for Q47746 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q47746
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 55.709α = 101.34
b = 77.319β = 108.13
c = 85.865γ = 90.06
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PHENIXrefinement
SCALAdata scaling
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Structure summary