6TMN | pdb_00006tmn

Structures of two thermolysin-inhibitor complexes that differ by a single hydrogen bond

• PDB DOI: https://doi.org/10.2210/pdb6TMN/pdb

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


• Deposited: 1987-06-29 Released: 1989-01-09 
• Deposition Author(s): Tronrud, D.E., Holden, H.M., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Structures of two thermolysin-inhibitor complexes that differ by a single hydrogen bond.

Tronrud, D.E., Holden, H.M., Matthews, B.W.

(1987) Science 235: 571-574

• PubMed: 3810156 
• DOI: https://doi.org/10.1126/science.3810156
• Primary Citation Related Structures: 
  6TMN


• PubMed Abstract: 
  

  The mode of binding to thermolysin of the ester analog Cbz-GlyP-(O)-Leu-Leu has been determined by x-ray crystallography and shown to be virtually identical (maximum difference 0.2 angstrom) with the corresponding peptide analog Cbz-GlyP-(NH)-Leu-Leu. The two inhibitors provide a matched pair of enzyme-inhibitor complexes that differ by 4.1 kilocalories per mole in intrinsic binding energy but are essentially identical except for the presence or absence of a specific hydrogen bond.

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: 35.06 kDa 
• Atom Count: 2,639 
• 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	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0PI	B [auth E]	N-[(2R,4S)-4-hydroxy-2-(2-methylpropyl)-4-oxido-7-oxo-9-phenyl-3,8-dioxa-6-aza-4-phosphanonan-1-oyl]-L-leucine C21 H33 N2 O8 P WPUXZWKBJRFUJC-ROUUACIJSA-N
ZN	G [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

Binding Affinity Annotations
ID	Source	Binding Affinity
0PI	BindingDB:  6TMN	Ki: 8910 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000655 (0PI)	B [auth E]	CBZ-GLYP-(O)-LEU-LEU (ZGP(O)LL)	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.1	α = 90
b = 94.1	β = 90
c = 131.4	γ = 120

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1989-01-09 
Deposition Author(s): Tronrud, D.E., Holden, H.M., Matthews, B.W.

Revision History  

• Version 1.0: 1989-01-09
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 2.0: 2022-11-23
  Type: Remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2024-05-22
  Changes: Data collection