1KRO

Thermolysin complexed with Z-D-Threonine (benzyloxycarbonyl-D-Threonine)

Structural Biology Knowledgebase: 1KRO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.182
  • R-Value Work: 0.166

Literature

Macromolecules
Sequence Display for 1KRO

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 34876.05

Macromolecule Entities
Molecule Chains Length Organism Details
Thermolysin A 316 Bacillus thermoproteolyticus EC#: 3.4.24.27 IUBMB
Mutation: D37N, E119Q
Gene Name(s): npr
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A benzyl chlorocarbonate
C8 H7 Cl O2
HSDAJNMJOMSNEV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DTH
Query on DTH

A D-THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-STHAYSLISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.182
  • R-Value Work: 0.166
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.76 α = 90.00
b = 93.76 β = 90.00
c = 131.34 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-10
  • Released Date: 2003-01-10
  • Deposition author(s): Senda, M., Senda, T., Kidokoro, S.

Revision History

  • 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