4DQD

The crystal structure of a transporter in complex with 3-phenylpyruvic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.162
  • R-Value Work: 0.143

Literature

Macromolecules
Sequence Display for 4DQD

Classification: SIGNALING PROTEIN

Total Structure Weight: 39783.02

Macromolecule Entities
Molecule Chains Length Organism Details
Extracellular ligand-binding receptor A 363 Rhodopseudomonas palustris Gene Name(s): RPB_4630
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PG4
Query on PG4

A TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PPY
Query on PPY

A 3-PHENYLPYRUVIC ACID
C9 H8 O3
BTNMPGBKDVTSJY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3PY
Query on 3PY

A 3-HYDROXYPYRUVIC ACID
C3 H4 O4
HHDDCCUIIUWNGJ-UHFFFAOYSA-N
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)
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: 1.6 Å
  • R-Value Free: 0.162
  • R-Value Work: 0.143
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 125.04 α = 90.00
b = 62.42 β = 113.67
c = 60.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-15
  • Released Date: 2012-02-29
  • Deposition author(s): Tan, K., Mack, J.C., Zerbs, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2012-02-29

    Type: Initial release

  • Version 1_1: 2013-05-15

    Type: Database references

  • Version 1_2: 2013-09-25

    Type: Database references