6Y4I | pdb_00006y4i

Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

• PDB DOI: https://doi.org/10.2210/pdb6Y4I/pdb

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


• Deposited: 2020-02-21 Released: 2021-03-31 
• Deposition Author(s): Kljajic, M., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.140 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.127 (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.

Macromolecule Content 

• Total Structure Weight: 35.55 kDa 
• Atom Count: 2,919 
• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0PK (Subject of Investigation/LOI)	K [auth E]	N-[(S)-[(1R)-1-{[(benzyloxy)carbonyl]amino}-2-phenylethyl](hydroxy)phosphoryl]-L-leucyl-L-alanine C25 H34 N3 O7 P PREBTZMCCRSQJI-YUXAGFNASA-N
CS	L [auth E]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N
DMS	G [auth E], H [auth E], I [auth E], J [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

Binding Affinity Annotations
ID	Source	Binding Affinity
0PK	BindingDB:  6Y4I	Ki: 0.07 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000656 (0PK)	K [auth E]	CBZ-PHE-P-LEU-ALA (ZFPLA)	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free:  0.140 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.612	α = 90
b = 92.612	β = 90
c = 129.969	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: 2021-03-31 
Deposition Author(s): Kljajic, M., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description