1TLX

THERMOLYSIN (NATIVE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol.

English, A.C.Done, S.H.Caves, L.S.Groom, C.R.Hubbard, R.E.

(1999) Proteins 37: 628-640

  • Primary Citation of Related Structures:  1TLI, 2TLI, 2TLX, 3TLI, 4TLI, 5TLI, 6TLI, 7TLI, 8TLI

  • PubMed Abstract: 
  • Multiple-solvent crystal structure determination (MSCS) allows the position and orientation of bound solvent fragments to be identified by determining the structure of protein crystals soaked in organic solvents. We have extended this technique by th ...

    Multiple-solvent crystal structure determination (MSCS) allows the position and orientation of bound solvent fragments to be identified by determining the structure of protein crystals soaked in organic solvents. We have extended this technique by the determination of high-resolution crystal structures of thermolysin (TLN), generated from crystals soaked in 2% to 100% isopropanol. The procedure causes only minor changes to the conformation of the protein, and an increasing number of isopropanol interaction sites could be identified as the solvent concentration is increased. Isopropanol occupies all four of the main subsites in the active site, although this was only observed at very high concentrations of isopropanol for three of the four subsites. Analysis of the isopropanol positions shows little correlation with interaction energy computed using a molecular mechanics force field, but the experimentally determined positions of isopropanol are consistent with the structures of known protein-ligand complexes of TLN.


    Related Citations: 
    • Structural Analysis of Zinc Substitutions in the Active Site of Thermolysin
      Holland, D.R.,Hausrath, A.C.,Juers, D.,Matthews, B.W.
      (1995) Protein Sci. 4: 1955
    • Structure of Thermolysin Refined at 1.6 Angstrom Resolution
      Holmes, M.A.,Matthews, B.W.
      (1982) J.Mol.Biol. 4: 623


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THERMOLYSIN
A
316Bacillus thermoproteolyticusGene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

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Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
VAL
Query on VAL

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Download CCD File 
A
VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.153 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.910α = 90.00
b = 93.910β = 90.00
c = 131.170γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-13
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance