1VNB - JenaLib

Title :   PROTON NUCLEAR MAGNETIC RESONANCE AND DISTANCE GEOMETRY(SLASH)SIMULATED ANNEALING STUDIES ON THE VARIANT-1 NEUROTOXIN FROM THE NEW WORLD SCORPION CENTRUROIDES SCULPTURATUS EWING

Authors :   W. Lee, N. R. Krishna

Date :   26 Oct 93 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A

Keywords :   Neurotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Lee, M. J. Jablonsky, D. D. Watt, N. R. Krishna
Proton Nuclear Magnetic Resonance And Distance Geometry/Simulated Annealing Studies On The Variant-1 Neurotoxin From The New World Scorpion Centruroides Sculpturatus Ewing.
Biochemistry V. 33 2468 1994
PubMed-ID: 8117707 | Reference-DOI: 10.1021/BI00175A015
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

NMR Structure (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SCX1_CENSC_002 *	K	26	N	SCX1_CENSC	---	---	A	K	7	N
2	UniProt	VAR_SCX1_CENSC_003 *	D	29	T	SCX1_CENSC	---	---	A	D	10	T
3	UniProt	VAR_SCX1_CENSC_004 *	K	40	E	SCX1_CENSC	---	---	A	K	21	E
4	UniProt	VAR_SCX1_CENSC_005 *	H	43	G	SCX1_CENSC	---	---	A	H	24	G
5	UniProt	VAR_SCX1_CENSC_006 *	T	46	K	SCX1_CENSC	---	---	A	T	27	K
6	UniProt	VAR_SCX1_CENSC_007 *	T	46	L	SCX1_CENSC	---	---	A	T	27	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

NMR Structure

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 SCX1_CENSC | P01492 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:65
                                    29        39        49        59        69        79     
            SCX1_CENSC   20 KEGYLVKKSDGCKYDCFWLGKNEHCDTECKAKNQGGSYGYCYAFACWCEGLPESTPTYPLPNKSC 84
               SCOP domains d1vnba_ A: Scorpion toxin                                         SCOP domains
               CATH domains 1vnbA00 A:1-65  [code=3.30.30.10, no name defined]                CATH domains
               Pfam domains Toxin_3-1vnbA01 A:1-55                                 ---------- Pfam domains
         Sec.struct. author .eee...................hhhhhhhh......eeee....eeee................ Sec.struct. author
             SAPs(SNPs) (1) ------N--T----------E--G--K-------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------L-------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  1vnb A  1 KEGYLVKKSDGCKYDCFWLGKNEHCNTECKAKNQGGSYGYCYAFACWCEGLPESTPTYPLPNKSC 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 (1, 1)

Pfam Domains (1, 1)

Gene Ontology (3, 3)

NMR Structure(hide GO term definitions)

Chain A (SCX1_CENSC | P01492)

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

NMR Structure
	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
(no "Ligands, Modified Residues, Ions" information available for 1vnb)

	Sites
(no "Sites" information available for 1vnb)

	Cis Peptide Bonds
		Tyr A:58 - Pro A:59	[ RasMol ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models 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)
Midas
	spacefill [ mono GIF format \| stereo GIF format ]
	sticks [ mono GIF format \| stereo GIF format ]
Setor
	ribbon, SS bonds, labeling [ mono GIF format \| stereo GIF format ]
	spacefill [ mono GIF format \| stereo GIF format ]
	ribbon, SS bonds, labeling [ mono GIF format \| stereo GIF format ]
	ribbon, secondary structure, SS bonds, labeling [ mono GIF format \| stereo GIF format ]

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1vnb
		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
	SCX1_CENSC \| P01492
		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
	SCX1_CENSC \| P01492
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description