Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34930.50 
• Atom Count: 2484 
• Residue Count: 316 
• Unique protein chains: 1

1TLX

THERMOLYSIN (NATIVE)

• DOI: 10.2210/pdb1TLX/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus thermoproteolyticus


• Deposited: 1998-11-02 Released: 2000-03-13 
• Deposition Author(s): English, A.C., Done, S.H., Groom, C.R., Hubbard, R.E.

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Experimental Data Snapshot

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

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

• PubMed: 10651278 
• Primary Citation of Related Structures:  
  8TLI, 7TLI, 6TLI, 5TLI, 4TLI, 3TLI, 2TLX, 2TLI, 1TLI


• 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 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.

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Related Citations: 

• Structure of Thermolysin Refined at 1.6 Angstrom Resolution
  Holmes, M.A.,Matthews, B.W.
  (1982) J.Mol.Biol. 4: 623
• 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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
THERMOLYSIN	A	316	Bacillus thermoproteolyticus	Mutation(s): 0  Gene Names: npr EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus) Go to UniProtKB:  P00800

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
LYS	A	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL	A	VALINE C5 H11 N O2 KZSNJWFQEVHDMF-BYPYZUCNSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

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 = 93.910	α = 90.00
b = 93.910	β = 90.00
c = 131.170	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-11-02 
• Released Date: 2000-03-13 
• Deposition Author(s): English, A.C., Done, S.H., Groom, C.R., Hubbard, R.E.

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