4TLN

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/bi00527a026
Primary Citation of Related Structures:
4TLN, 5TLN

Macromolecule Content

Total Structure Weight: 34.73 kDa
Atom Count: 2,597
Modelled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00800
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LNO Query on LNO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	L-LEUCYL-HYDROXYLAMINE C₆ H₁₄ N₂ O₂ UJJHPFLWSVFLBE-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
LNO	PDBBind: 4TLN	Ki: 1.90e+5 (nM) from 1 assay(s)
	Binding MOAD: 4TLN	Ki: 1.90e+5 (nM) from 1 assay(s)
	BindingDB: 4TLN	Kd: 1.91e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Observed: 0.169
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

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Entry History

Deposition Data

Released Date: 1982-05-26

Deposition Author(s):

Matthews, B.W.

Holmes, M.A.

Revision History (Full details and data files)

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

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Help and Resources

4TLN

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)