5BMQ

Crystal structure of L,D-transpeptidase (Yku) from Stackebrandtia nassauensis

Structural Biology Knowledgebase: 5BMQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.178
  • R-Value Work: 0.154

Literature

Macromolecules
Sequence Display for 5BMQ

Classification: HYDROLASE

Total Structure Weight: 27405.93

Macromolecule Entities
Molecule Chains Length Organism Details
ErfK/YbiS/YcfS/YnhG family protein A 243 Stackebrandtia nassauensis EC#: 3 IUBMB
Gene Name(s): Snas_6095
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DIO
Query on DIO

A 1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.178
  • R-Value Work: 0.154
  • Space Group: I 21 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 143.36 α = 90.00
b = 143.36 β = 90.00
c = 143.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-05-22
  • Released Date: 2015-06-03
  • Deposition author(s): Chang, C., Bigelow, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

No revisions since initial release