2ASC

Scorpion toxin LQH-alpha-IT

PDB DOI: https://doi.org/10.2210/pdb2ASC/pdb

Classification: TOXIN
Organism(s): Leiurus quinquestriatus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2005-08-23 Released: 2006-09-05
Deposition Author(s): Kahn, R., Karbat, I., Gurevitz, M., Frolow, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.138 (Depositor), 0.140 (DCC)
R-Value Work:
0.130 (Depositor), 0.130 (DCC)
R-Value Observed:
0.131 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

X-ray structures of Lqh-alpha-IT and Lqh-alpha-IT8D9D10V mutant

Kahn, R., Karbat, I., Gurevitz, M., Frolow, F.

To be published.

Macromolecule Content

Total Structure Weight: 8.46 kDa
Atom Count: 690
Modelled Residue Count: 65
Deposited Residue Count: 65
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
neurotoxin alpha-IT	A	65	Leiurus quinquestriatus	Mutation(s): 0
UniProt
Find proteins for P17728 (Leiurus hebraeus) Explore P17728 Go to UniProtKB: P17728
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17728
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DR0 Query on DR0 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-(HYDROXYMETHYL)-N,N-DIMETHYLHEXAN-1-AMINIUM C₉ H₂₂ N O HSCKPPPLTPBXED-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DR8 Query on DR8 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N,N,N-TRIMETHYLHEPTA-1,3,5-TRIYN-1-AMINIUM C₁₀ H₁₂ N AKYJILYZPCHMQA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A]	O [auth A], P [auth A], R [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
MOH Query on MOH Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A]	N [auth A], Q [auth A], S [auth A]	METHANOL C H₄ O OKKJLVBELUTLKV-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain Q [auth A] Focus chain S [auth A] Interactions & Density Focus chain N [auth A] Focus chain Q [auth A] Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.138 (Depositor), 0.140 (DCC)
R-Value Work: 0.130 (Depositor), 0.130 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.714	α = 90
b = 129.714	β = 90
c = 129.714	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
BEAST	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-09-05
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2019-10-16
Changes: Data collection, Derived calculations
Version 1.5: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.6: 2024-10-30
Changes: Structure summary