1KDY

Pseudomonas serine-carboxyl proteinase complexed with the inhibitor AIPF (this enzyme renamed "sedolisin" in 2003)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.155
  • R-Value Work: 0.134

Literature

Macromolecules
Sequence Display for 1KDY

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 38954.87

Macromolecule Entities
Molecule Chains Length Organism Details
SERINE-CARBOXYL PROTEINASE A 370 Pseudomonas sp. EC#: 3.4.21.100 IUBMB
Gene Name(s): pcp
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
AIPF PEPTIDE INHIBITOR B 4 synthetic

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

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000240
Query on PRD_000240
B N-acetyl-L-isoleucyl-L-prolyl-L-Phenylalaninal Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.155
  • R-Value Work: 0.134
  • Space Group: P 62

Unit Cell:

Length (Å) Angle (°)
a = 97.29 α = 90.00
b = 97.29 β = 90.00
c = 83.46 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-13
  • Released Date: 2001-12-12
  • Deposition author(s): Wlodawer, A., Li, M., Gustchina, A., Dauter, Z., Uchida, K., Oyama, H., Glodfarb, N.E., Dunn, B.M., Oda, K.

Revision History

  • Version 1_0: 2001-12-12

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance

  • Version 1_3: 2012-12-12

    Type: Other