1ZDP

Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-thiorphan

Structural Biology Knowledgebase: 1ZDP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Observed: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1ZDP

Classification: HYDROLASE

Total Structure Weight: 34841.62

Macromolecule Entities
Molecule Chains Length Organism Details
Thermolysin E 316 Bacillus thermoproteolyticus EC#: 3.4.24.27 IUBMB
Mutation: N37D, Q119E, K177E
Gene Name(s): npr

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

E (2-MERCAPTOMETHYL-3-PHENYL-PROPIONYL)-GLYCINE
THIORPHAN (Synonym)
C12 H15 N O3 S
LJJKNPQAGWVLDQ-SNVBAGLBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

E CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TIO IC50: 1800 - 9500 nM (99) BindingDB
Ki: 1800 nM (99) BindingDB

Ki: 1800 nM  BindingMOAD
Ki: 1800 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Observed: 0.183
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.00 α = 90.00
b = 94.00 β = 90.00
c = 132.10 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-04-14
  • Released Date: 2005-04-26
  • Deposition author(s): Roderick, S.L., Fournie-Zaluski, M.C., Roques, B.P., Matthews, B.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4