1VXR - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   O-ETHYLMETHYLPHOSPHONYLATED ACETYLCHOLINESTERASE OBTAINED BY REACTION WITH O-ETHYL-S-[2-[BIS(1-METHYLETHYL)AMINO]ETHYL] METHYLPHOSPHONOTHIOATE (VX)

Authors :   C. B. Millard, G. Koellner, I. Silman, J. L. Sussman

Date :   21 Apr 99 (Deposition) - 15 Nov 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Cholinesterase, Organophosphate, Serine Hydrolase, Chemical-Warfare, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. B. Millard, G. Koellner, A. Ordentlich, A. Shafferman, I. Silman, J. L. Sussman
Reaction Products Of Acetylcholinesterase And Vx Reveal A Mobile Histidine In The Catalytic Triad
J. Am. Chem. Soc. V. 121 9883 1999
PubMed: search | Reference-DOI: 10.1021/JA992704I

Molecule 1 - PROTEIN (ACETYLCHOLINESTERASE)
	Cellular Location	:	MEMBRANE BOUND BY GPI ANCHOR
	Chains	:	A
	EC Number	:	3.1.1.7
	Organ	:	ELECTRIC ORGAN
	Organism Common	:	PACIFIC ELECTRIC RAY
	Organism Scientific	:	TORPEDO CALIFORNICA
	Organism Taxid	:	7787
	Other Details	:	COMPLEXED WITH THE NERVE AGENT VX
	Tissue	:	ELECTROPLAQUE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	VX	1	Ligand/Ion	O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:59 , SER A:61	BINDING SITE FOR RESIDUE NDG A 9010
2	AC2	SOFTWARE	ASN A:416 , HOH A:1298 , NAG A:9021	BINDING SITE FOR RESIDUE NAG A 9020
3	AC3	SOFTWARE	NAG A:9020	BINDING SITE FOR RESIDUE NAG A 9021
4	AC4	SOFTWARE	GLY A:118 , GLY A:119 , SER A:200 , ALA A:201 , PHE A:288 , PHE A:331 , HIS A:440	BINDING SITE FOR RESIDUE VX A 999
5	AC5	SOFTWARE	THR A:10 , LYS A:11 , ARG A:243 , GLU A:247 , ASN A:280 , VAL A:281 , LEU A:282 , PRO A:283	BINDING SITE FOR RESIDUE MES A 8010
6	AC6	SOFTWARE	MET A:405 , HIS A:406 , ASN A:409 , GLN A:500 , CYS A:521 , VAL A:522 , ASN A:525 , HOH A:1047 , HOH A:1200	BINDING SITE FOR RESIDUE MES A 8020
7	CAT	AUTHOR	SER A:200 , HIS A:440 , GLU A:327	CATALYTIC TRIAD
8	OXY	AUTHOR	GLY A:118 , GLY A:119 , ALA A:201	CATALYTIC OXYANION HOLE

Asymmetric/Biological Unit

No.	Residues
1	A:67	-	A:94
2	A:254	-	A:265
3	A:402	-	A:521

Asymmetric/Biological Unit

No.	Residues
1	Ser A:103	-	Pro A:104

(no "SAP(SNP)/Variant" information available for 1VXR)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYLESTERASE_B_2	PS00941	Carboxylesterases type-B signature 2.	ACES_TETCF	113-123	1	A:92-102
2	CARBOXYLESTERASE_B_1	PS00122	Carboxylesterases type-B serine active site.	ACES_TETCF	208-223	1	A:187-202

(no "Exon" information available for 1VXR)

Asymmetric/Biological 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:532
 aligned with ACES_TETCF | P04058 from UniProtKB/Swiss-Prot  Length:586

    Alignment length:532
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554  
           ACES_TETCF    25 SELLVNTKSGKVMGTRVPVLSSHISAFLGIPFAEPPVGNMRFRRPEPKKPWSGVWNASTYPNNCQQYVDEQFPGFSGSEMWNPNREMSEDCLYLNIWVPSPRPKSTTVMVWIYGGGFYSGSSTLDVYNGKYLAYTEEVVLVSLSYRVGAFGFLALHGSQEAPGNVGLLDQRMALQWVHDNIQFFGGDPKTVTIFGESAGGASVGMHILSPGSRDLFRRAILQSGSPNCPWASVSVAEGRRRAVELGRNLNCNLNSDEELIHCLREKKPQELIDVEWNVLPFDSIFRFSFVPVIDGEFFPTSLESMLNSGNFKKTQILLGVNKDEGSFFLLYGAPGFSKDSESKISREDFMSGVKLSVPHANDLGLDAVTLQYTDWMDDNNGIKNRDGLDDIVGDHNVICPLMHFVNKYTKFGNGTYLYFFNHRASNLVWPEWMGVIHGYEIEFVFGLPLVKELNYTAEEEALSRRIMHYWATFAKTGNPNEPHSQESKWPLFTTKEQKFIDLNTEPMKVHQRLRVQMCVFWNQFLPKLLNAT 556
               SCOP domains d1vxra_ A: Acetylcholinesterase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1vxrA00 A:4-535  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeeeeeee....eeeeeeeee......................eeee..................hhhhhhh..........eeeeeee......eeeeeeee...............hhhhhhhh..eeeeee....................hhhhhhhhhhhhhhhh.........eeeeeeehhhhhhhhhhhh........eeeeeee...........hhhhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhh..........................hhhhhhh......eeeeeee....hhhhhhh.............hhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...................hhhhhh...........hhhhhhhhhhhhhhhhhhhh......................eeee....eeeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------CARBOXYLEST------------------------------------------------------------------------------------CARBOXYLESTERASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vxr A   4 SELLVNTKSGKVMGTRVPVLSSHISAFLGIPFAEPPVGNMRFRRPEPKKPWSGVWNASTYPNNCQQYVDEQFPGFSGSEMWNPNREMSEDCLYLNIWVPSPRPKSTTVMVWIYGGGFYSGSSTLDVYNGKYLAYTEEVVLVSLSYRVGAFGFLALHGSQEAPGNVGLLDQRMALQWVHDNIQFFGGDPKTVTIFGESAGGASVGMHILSPGSRDLFRRAILQSGSPNCPWASVSVAEGRRRAVELGRNLNCNLNSDEELIHCLREKKPQELIDVEWNVLPFDSIFRFSFVPVIDGEFFPTSLESMLNSGNFKKTQILLGVNKDEGSFFLLYGAPGFSKDSESKISREDFMSGVKLSVPHANDLGLDAVTLQYTDWMDDNNGIKNRDGLDDIVGDHNVICPLMHFVNKYTKFGNGTYLYFFNHRASNLVWPEWMGVIHGYEIEFVFGLPLVKELNYTAEEEALSRRIMHYWATFAKTGNPNEPHSQESKWPLFTTKEQKFIDLNTEPMKVHQRLRVQMCVFWNQFLPKLLNAT 535
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: Acetylcholinesterase-like (219)

Protein domain: Acetylcholinesterase (107)

Pacific electric ray (Torpedo californica) [TaxId: 7787] (75)

d1vxra_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1820, no name defined] (692)

Pacific electric ray (Torpedo californica) (75)

1vxrA00

A:4-535

(no "Pfam Domain" information available for 1VXR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ACES_TETCF | P04058)

molecular function
	GO:0003990	acetylcholinesterase activity	Catalysis of the reaction: acetylcholine + H2O = choline + acetate.
	GO:0052689	carboxylic ester hydrolase activity	Catalysis of the hydrolysis of a carboxylic ester bond.
	GO:0004104	cholinesterase activity	Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
	GO:0001507	acetylcholine catabolic process in synaptic cleft	The chemical reactions and pathways resulting in the breakdown of acetylcholine that occurs in the synaptic cleft during synaptic transmission.
	GO:0042135	neurotransmitter catabolic process	The chemical reactions and pathways resulting in the breakdown of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.
cellular component
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
	GO:0043083	synaptic cleft	The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.

Asymmetric/Biological 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
		MES	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		VX	[ 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 ]
		CAT	[ RasMol ]	+environment [ RasMol ]
		OXY	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser A:103 - Pro A:104	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - 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)

Access by PDB/NDB ID
	1vxr
		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
	ACES_TETCF \| P04058
		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)
	3.1.1.7
		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

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
	ACES_TETCF \| P04058
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1VXR)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (8, 8)

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File