2YEO - JenaLib

Title :   A39L MUTATION OF SCORPION TOXIN LQH-ALPHA-IT

Authors :   F. Frolow, R. Kahn, M. Gurevitz

Date :   28 Mar 11 (Deposition) - 13 Apr 11 (Release) - 18 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.08

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Toxin, Defense Response (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Frolow, R. Kahn, M. Gurevitz
Crystal Structures Of Scorpion Alpha-Toxinsmutants Reveal Conformational Constraints That Dictate Preference For Mammalian Brain Voltage-Gated Na- Channels
To Be Published
PubMed: search

Compounds

Molecule 1 - ALPHA-INSECT TOXIN LQHAIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 20-83
	Mutation	:	YES
	Organism Common	:	SCORPION
	Organism Scientific	:	LEIURUS QUINQUESTRIATUS HEBRAEUS
	Organism Taxid	:	6884
	Other Details	:	SCORPION TOXIN
	Synonym	:	MUTANT OF NEUROTOXIN ALPHA-IT, LQH-ALPHA-IT, ALPHA-IT

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	DR0	1	Ligand/Ion	N-(HYDROXYMETHYL)-N,N-DIMETHYLHEXAN-1-AMINIUM
3	DR8	1	Ligand/Ion	N,N,N-TRIMETHYLHEPTA-1,3,5-TRIYN-1-AMINIUM
4	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DR0	3	Ligand/Ion	N-(HYDROXYMETHYL)-N,N-DIMETHYLHEXAN-1-AMINIUM
3	DR8	3	Ligand/Ion	N,N,N-TRIMETHYLHEPTA-1,3,5-TRIYN-1-AMINIUM
4	EDO	12	Ligand/Ion	1,2-ETHANEDIOL

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:36 , TYR A:50	BINDING SITE FOR RESIDUE DR8 A1066
2	AC2	SOFTWARE	ASP A:20 , TYR A:36 , CYS A:37 , TRP A:39 , CL A:1071 , EDO A:1074 , HOH A:2071	BINDING SITE FOR RESIDUE DR0 A1067
3	AC3	SOFTWARE	ASP A:20 , ASN A:24 , GLY A:35 , TYR A:36 , TRP A:48 , EDO A:1069 , HOH A:2084	BINDING SITE FOR RESIDUE EDO A1068
4	AC4	SOFTWARE	TYR A:6 , ASP A:20 , ALA A:21 , ASN A:24 , EDO A:1068 , HOH A:2057 , HOH A:2104	BINDING SITE FOR RESIDUE EDO A1069
5	AC5	SOFTWARE	VAL A:14 , ARG A:59 , CYS A:64	BINDING SITE FOR RESIDUE CL A1070
6	AC6	SOFTWARE	TRP A:39 , DR0 A:1067 , HOH A:2071	BINDING SITE FOR RESIDUE CL A1071
7	AC7	SOFTWARE	ILE A:7 , ALA A:8 , LYS A:9 , TYR A:15 , ASN A:30 , VAL A:56 , HOH A:2105 , HOH A:2106	BINDING SITE FOR RESIDUE EDO A1072
8	AC8	SOFTWARE	ARG A:19 , HOH A:2051	BINDING SITE FOR RESIDUE CL A1073
9	AC9	SOFTWARE	PHE A:18 , ARG A:19 , TRP A:39 , LEU A:40 , DR0 A:1067 , HOH A:2107 , HOH A:2108	BINDING SITE FOR RESIDUE EDO A1074

SS Bonds (4, 4)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:65
 aligned with SCXA_LEIQH | P17728 from UniProtKB/Swiss-Prot  Length:85

    Alignment length:65
                                    28        38        48        58        68        78     
            SCXA_LEIQH   19 SVRDAYIAKNYNCVYECFRDAYCNELCTKNGASSGYCQWAGKYGNACWCYALPDNVPIRVPGKCH 83
               SCOP domains d2yeoa_ A: automated matches                                      SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains --Toxin_3-2yeoA01 A:3-56                                --------- Pfam domains
         Sec.struct. author .eeeee.ee...ee....hhhhhhhhhhhh...eeeeeeee..eeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  2yeo A  1 MVRDAYIAKNYNCVYECFRDAYCNELCTKNGASSGYCQWLGKYGNACWCYALPDNVPIRVPGKCR 65
                                    10        20        30        40        50        60

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (3, 3)

Asymmetric Unit(hide GO term definitions)

Chain A (SCXA_LEIQH | P17728)

molecular function
	GO:0008200	ion channel inhibitor activity	Stops, prevents, or reduces the activity of an ion channel.
biological process
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DR0	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DR8	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:10 - Tyr A:11	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2yeo
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SCXA_LEIQH \| P17728
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SCXA_LEIQH \| P17728
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description