4E3Q

PMP-bound form of Aminotransferase crystal structure from Vibrio fluvialis

Structural Biology Knowledgebase: 4E3Q SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4E3Q

Classification: TRANSFERASE

Total Structure Weight: 213887.22

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate transaminase A, B, C, D 473 Vibrio fluvialis Gene Name(s):

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PMP
Query on PMP

A, B, C, D 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
PYRIDOXAMINE-5'-PHOSPHATE (Synonym)
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BEN
Query on BEN

A, B BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A, B, C, D SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.174
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 63.07 α = 90.00
b = 162.18 β = 90.00
c = 180.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-10
  • Released Date: 2012-10-10
  • Deposition author(s): Midelfort, K.S., Kumar, R., Han, S., Karmilowicz, M.J., McConnell, K., Gehlhaar, D.K., Mistry, A., Chang, J.S., Anderson, M., Vilalobos, A., Minshull, J., Govindarajan, S., Wong, J.W.

Revision History

  • 2013-01-02
    Type: Citation | Details: Citation update