1KCD

Endopolygalacturonase I from Stereum purpureum complexed with two galacturonate at 1.15 A resolution.

Structural Biology Knowledgebase: 1KCD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.163
  • R-Value Work: 0.126

Literature

Macromolecules
Sequence Display for 1KCD

Classification: HYDROLASE

Total Structure Weight: 35518.80

Macromolecule Entities
Molecule Chains Length Organism Details
ENDOPOLYGALACTURONASE A 335 Chondrostereum purpureum EC#: 3.2.1.15 IUBMB
Fragment: residues 1-335
Gene Name(s): cppg1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GTK
Query on GTK

A beta-D-galactofuranuronic acid
C6 H10 O7
OEVWLAOZEALENB-ORELYVPDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GTR
Query on GTR

A Beta-D-Galactopyranuronic acid
Galacturonic acid (Synonym)
C6 H10 O7
AEMOLEFTQBMNLQ-DTEWXJGMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.163
  • R-Value Work: 0.126
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 46.50 α = 72.39
b = 52.07 β = 69.50
c = 37.23 γ = 70.54

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-08
  • Released Date: 2002-06-05
  • Deposition author(s): Shimizu, T., Nakatsu, T., Miyairi, K., Okuno, T., Kato, H.

Revision History

  • 2015-10-14
    Type: Non-polymer description | Details: update GTR
  • 2011-08-24
    Type: Non-polymer description | Details: update GTR 1001 to GTK 1001
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4