4H57

Thermolysin inhibition

• PDB DOI: https://doi.org/10.2210/pdb4H57/pdb
• Entry: 4H57 supersedes: 3FWD

• Classification: HYDROLASE/HYDROLASE inhibitor
• Organism(s): Bacillus thermoproteolyticus
• Mutation(s): No 


• Deposited: 2012-09-18 Released: 2012-10-03 
• Deposition Author(s): Englert, L., Biela, A., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.167 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 

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

• PubMed: 23283700 
• DOI: https://doi.org/10.1002/anie.201208561
• Primary Citation of Related Structures:  
  4H57

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.65 kDa 
• Atom Count: 2,880 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A	316	Bacillus thermoproteolyticus	Mutation(s): 0  EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0PJ	G [auth A]	N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-leucine C21 H34 N3 O7 P ASUDVBNLLSQCDJ-ROUUACIJSA-N
GOL	H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	K [auth A], L [auth A], M [auth A], N [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0PJ	BindingDB:  4H57	Ki: 1.00e+14 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000654 (0PJ)	G [auth A]	CBZ-GLY-P-LEU-LEU (ZGPLL)	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.167 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.452	α = 90
b = 92.452	β = 90
c = 129.778	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Englert, L., Biela, A., Heine, A., Klebe, G.
• This entry supersedes: 3FWD

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2013-02-27
  Changes: Other
• Version 1.2: 2013-03-06
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description