6YMR | pdb_00006ymr

Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

• PDB DOI: https://doi.org/10.2210/pdb6YMR/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Geobacillus stearothermophilus
• Mutation(s): No 


• Deposited: 2020-04-09 Released: 2021-04-21 
• Deposition Author(s): Kljajic, M., Heine, A., Klebe, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

Kljajic, M., Gerber, H.-D., Heine, A., Klebe, G.

To be published.

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: 35.25 kDa 
• Atom Count: 2,783 
• Modeled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A [auth E]	316	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: nprS, nprM EC: 3.4.24.27
UniProt
Find proteins for P43133 (Geobacillus stearothermophilus) Explore P43133  Go to UniProtKB:  P43133

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OZE (Subject of Investigation/LOI)	I [auth E]	(((R)-1-(((benzyloxy)carbonyl)amino)-2-phenylethyl)oxidophosphoryl)glycyl-L-leucinate C24 H32 N3 O7 P YJSHTZYDPJRJOL-RBBKRZOGSA-N
DMS	G [auth E], H [auth E]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth E], D [auth E], E, F [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.768	α = 90
b = 92.768	β = 90
c = 129.602	γ = 120

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Kljajic, M., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description