4TLN | pdb_00004tln

BINDING OF HYDROXAMIC ACID INHIBITORS TO CRYSTALLINE THERMOLYSIN SUGGESTS A PENTACOORDINATE ZINC INTERMEDIATE IN CATALYSIS

• PDB DOI: https://doi.org/10.2210/pdb4TLN/pdb

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


• Deposited: 1982-02-08 Released: 1982-05-26 
• Deposition Author(s): Matthews, B.W., Holmes, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 
  0.156 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Binding of hydroxamic acid inhibitors to crystalline thermolysin suggests a pentacoordinate zinc intermediate in catalysis.

Holmes, M.A., Matthews, B.W.

(1981) Biochemistry 20: 6912-6920

• PubMed: 7317361 
• DOI: https://doi.org/10.1021/bi00527a026
• Primary Citation Related Structures: 
  4TLN, 5TLN

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.73 kDa 
• Atom Count: 2,597 
• 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	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
LNO	G [auth A]	L-LEUCYL-HYDROXYLAMINE C6 H14 N2 O2 UJJHPFLWSVFLBE-YFKPBYRVSA-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
LNO	BindingDB:  4TLN	Ki: 1.90e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work:  0.156 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.2	α = 90
b = 94.2	β = 90
c = 131.4	γ = 120

Software Package:

Software Name	Purpose
TNT	refinement
VENUS	data reduction
ODPROC	data scaling
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1982-05-26 
Deposition Author(s): Matthews, B.W., Holmes, M.A.

Revision History  

• Version 1.0: 1982-05-26
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2019-07-17
  Changes: Data collection, Refinement description
• 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