1KJP

Thermolysin complexed with Z-L-Glutamic acid (benzyloxycarbonyl-L-Glutamic acid)

Structural Biology Knowledgebase: 1KJP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.168

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1KJP

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 34904.06

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

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLU
Query on GLU

A GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.168
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.75 α = 90.00
b = 93.75 β = 90.00
c = 131.60 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-05
  • Released Date: 2002-12-05
  • 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