1YLH

Crystal Structure of Phosphoenolpyruvate Carboxykinase from Actinobaccilus succinogenes in Complex with Manganese and Pyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.190

Literature

Macromolecules
Sequence Display for 1YLH

Classification: LYASE

Total Structure Weight: 62724.19

Macromolecule Entities
Molecule Chains Length Organism Details
phosphoenolpyruvate carboxykinase A 560 Actinobacillus succinogenes EC#: 4.1.1.49 IUBMB
Gene Name(s): pckA Asuc_0221
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DT3
Query on DT3

A (2S,3S)-2,3-DIHYDROXY-4-SULFANYLBUTANE-1- SULFONATE
C4 H9 O5 S2
BJXWUWDPCVAQDI-QWWZWVQMSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PYR
Query on PYR

A PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.190
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 56.74 α = 90.00
b = 55.09 β = 106.17
c = 90.08 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-19
  • Released Date: 2005-06-28
  • Deposition author(s): Leduc, Y.A., Prasad, L., Laivenieks, M., Zeikus, J.G., Delbaere, L.T.

Revision History

  • Version 1_0: 2005-06-28

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance