1PYY

Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution

Structural Biology Knowledgebase: 1PYY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 1PYY

Classification: TRANSPEPTIDASE

Total Structure Weight: 77477.38

Macromolecule Entities
Molecule Chains Length Organism Details
Penicillin-binding protein 2X A 702 Streptococcus pneumoniae Mutation: T338A, M339F
Gene Name(s): pbpX spr0304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
OSU
Query on OSU

A N-OCTANOYLSUCROSE
SUCROSE MONOCAPROYLATE, (Synonym)
C20 H36 O12
AWSYOWHJNGZJGU-OASARBKBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.218
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 128.22 α = 90.00
b = 64.75 β = 118.89
c = 146.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-07-09
  • Released Date: 2003-09-30
  • Deposition author(s): Chesnel, L., Pernot, L., Lemaire, D., Champelovier, D., Croize, J., Dideberg, O., Vernet, T., Zapun, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name