4H57

Thermolysin inhibition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dissecting the hydrophobic effect on the molecular level: the role of water, enthalpy, and entropy in ligand binding to thermolysin.

Biela, A.Nasief, N.N.Betz, M.Heine, A.Hangauer, D.Klebe, G.

(2013) Angew.Chem.Int.Ed.Engl. 52: 1822-1828


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
A
316Bacillus thermoproteolyticusMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
0PJ
Query on 0PJ

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Download CCD File 
A
N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-leucine
ZGPLL
C21 H34 N3 O7 P
ASUDVBNLLSQCDJ-ROUUACIJSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000654 (0PJ)
Query on PRD_000654
ACBZ-GLY-P-LEU-LEU (ZGPLL)Peptide-like / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.148 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.452α = 90.00
b = 92.452β = 90.00
c = 129.778γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXmodel building
MAR345dtbdata collection
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Other
  • Version 1.2: 2013-03-06
    Type: Database references