6UE2

1.85 Angstrom Resolution Crystal Structure of Class D beta-lactamase from Clostridium difficile 630


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

1.85 Angstrom Resolution Crystal Structure of Class D beta-lactamase from Clostridium difficile 630.

Minasov, G.Shuvalova, L.Dubrovska, I.Rosas-Lemus, M.Jedrzejczak, R.Satchell, K.J.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B, C, D
255Clostridioides difficile (strain 630)Mutation(s): 0 
EC: 3.5.2.6
Find proteins for Q188Q3 (Clostridioides difficile (strain 630))
Go to UniProtKB:  Q188Q3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PPI
Query on PPI

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Download CCD File 
C
PROPANOIC ACID
C3 H6 O2
XBDQKXXYIPTUBI-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.983α = 90.00
b = 93.200β = 90.00
c = 137.583γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release