6YMS | pdb_00006yms

Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

• PDB DOI: https://doi.org/10.2210/pdb6YMS/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.116 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.117 (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: 35.54 kDa 
• Atom Count: 2,959 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OZH (Subject of Investigation/LOI)	J [auth E]	(2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{S})-2-phenyl-1-(phenylmethoxycarbonylamino)ethyl]phosphoryl]amino]ethanoylamino]pentanoic acid C24 H32 N3 O7 P YJSHTZYDPJRJOL-UNMCSNQZSA-N
TRS	K [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	L [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	G [auth E], H [auth E], I [auth E]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	F [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth E], C [auth E], D [auth E], E	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.116 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.619	α = 90
b = 92.619	β = 90
c = 129.982	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