4RLG

The clear crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745

Structural Biology Knowledgebase: 4RLG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.191
  • R-Value Work: 0.162

Literature

Macromolecules
Sequence Display for 4RLG

Classification: LYASE

Total Structure Weight: 216914.38

Macromolecule Entities
Molecule Chains Length Organism Details
Pyridoxal-dependent decarboxylase A, B, C, D 486 Sphaerobacter thermophilus EC#: 4.1.1.15 IUBMB
Gene Name(s): Sthe_2364
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ABU
Query on ABU

D GAMMA-AMINO-BUTANOIC ACID
GAMMA(AMINO)-BUTYRIC ACID (Synonym)
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, B, C, D POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 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
LLP
Query on LLP
A, B, C, D L-PEPTIDE LINKING C14 H22 N3 O7 P LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.191
  • R-Value Work: 0.162
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.32 α = 90.00
b = 124.98 β = 99.49
c = 132.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-10-16
  • Released Date: 2014-10-29
  • Deposition author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

No revisions since initial release