2VL8 | pdb_00002vl8

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF LETHAL TOXIN FROM CLOSTRIDIUM SORDELLII IN COMPLEX WITH UDP, CASTANOSPERMINE AND CALCIUM ION

PDB DOI: https://doi.org/10.2210/pdb2VL8/pdb

Classification: TOXIN
Organism(s): Paraclostridium sordellii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-01-09 Released: 2008-06-17
Deposition Author(s): Jank, T., Ziegler, M.O.P., Schulz, G.E., Aktories, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.255 (Depositor), 0.251 (DCC)
R-Value Work:
0.217 (Depositor), 0.215 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Inhibition of the Glucosyltransferase Activity of Clostridial Rho/Ras-Glucosylating Toxins by Castanospermine.

Jank, T., Ziegler, M.O.P., Schulz, G.E., Aktories, K.

(2008) FEBS Lett 582: 2277

PubMed: 18505687 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2008.05.025
Primary Citation Related Structures:
2VL8

PubMed Abstract:
Castanospermine was identified as an inhibitor of the Rho/Ras-glucosylating Clostridium sordellii lethal toxin and Clostridium difficile toxin B. Microinjection of castanospermine into embryonic bovine lung cells prevented the cytotoxic effects of toxins. The crystal structure of the glucosyltransferase domain of C. sordellii lethal toxin in complex with castanospermine, UDP and a calcium ion was solved at a resolution of 2.3A. The inhibitor binds in a conformation that brings its four hydroxyl groups and its N-atom almost exactly in the positions of the four hydroxyls and of the ring oxygen of the glucosyl moiety of UDP-glucose, respectively.

Organizational Affiliation

Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Albert-Ludwigs-Universität, Albertstrasse 25, Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 192.8 kDa
Atom Count: 13,720
Modeled Residue Count: 1,609
Deposited Residue Count: 1,638
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOTOXIN L	A, B, C	546	Paraclostridium sordellii	Mutation(s): 2 EC: 3.4.22
UniProt
Find proteins for Q46342 (Paraclostridium sordellii) Explore Q46342 Go to UniProtKB: Q46342
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q46342
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], L [auth C]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C]
CTS Query on CTS Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], M [auth C]	CASTANOSPERMINE C₈ H₁₅ N O₄ JDVVGAQPNNXQDW-TVNFTVLESA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], K [auth B], N [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.255 (Depositor), 0.251 (DCC)
R-Value Work: 0.217 (Depositor), 0.215 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.689	α = 90
b = 191.332	β = 90
c = 205.384	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-06-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-06-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other