1KDY

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

Structural Biology Knowledgebase: 1KDY SBKB.org


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: 38955.25

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)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
B NON-POLYMER C2 H4 O --
PHL
Query on PHL
B L-PEPTIDE LINKING C9 H13 N O PHE

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
  • Electron Density Server: EDS EDS

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

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords