4DWB - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH [2-(N-PENTYLAMINO)ETHANE-1,1-DIYL]BISPHOSPHONIC ACID AND MG2+

Authors :   S. Aripirala, L. M. Amzel, S. B. Gabelli

Date :   24 Feb 12 (Deposition) - 16 Jan 13 (Release) - 17 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Geranyl Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Aripirala, S. H. Szajnman, J. Jakoncic, J. B. Rodriguez, R. Docampo S. B. Gabelli, L. M. Amzel
Design, Synthesis, Calorimetry, And Crystallographic Analysis Of 2-Alkylaminoethyl-1, 1-Bisphosphonates As Inhibitors Of Trypanosoma Cruzi Farnesyl Diphosphate Synthase.
J. Med. Chem. V. 55 6445 2012
PubMed-ID: 22715997 | Reference-DOI: 10.1021/JM300425Y

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
	Chains	:	A
	EC Number	:	2.5.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FPPS
	Organism Scientific	:	TRYPANOSOMA CRUZI
	Organism Taxid	:	5693
	Synonym	:	FPPS, FARNESYL DIPHOSPHATE SYNTHASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 9)

No.	Name	Count	Type	Full Name
1	0M7	1	Ligand/Ion	[2-(PENTYLAMINO)ETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)
2	ACT	1	Ligand/Ion	ACETATE ION
3	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
4	MG	3	Ligand/Ion	MAGNESIUM ION
5	NA	1	Ligand/Ion	SODIUM ION
6	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	0M7	2	Ligand/Ion	[2-(PENTYLAMINO)ETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)
2	ACT	2	Ligand/Ion	ACETATE ION
3	IPE	2	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION
6	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:47 , LYS A:48 , TYR A:49 , PHE A:50 , ARG A:51 , GLN A:91 , PHE A:246 , LYS A:264 , 0M7 A:509 , HOH A:610 , HOH A:612	BINDING SITE FOR RESIDUE IPE A 501
2	AC2	SOFTWARE	GLN A:21 , HIS A:141	BINDING SITE FOR RESIDUE SO4 A 502
3	AC3	SOFTWARE	ASP A:191 , ARG A:237 , GLU A:331 , SER A:334 , LEU A:335 , HOH A:653	BINDING SITE FOR RESIDUE SO4 A 503
4	AC4	SOFTWARE	HIS A:141 , TYR A:142 , HOH A:688	BINDING SITE FOR RESIDUE ACT A 504
5	AC5	SOFTWARE	ILE A:129 , LYS A:132 , SER A:133 , HOH A:625 , HOH A:633	BINDING SITE FOR RESIDUE NA A 505
6	AC6	SOFTWARE	ASP A:98 , ASP A:102 , ASP A:170 , MG A:507 , 0M7 A:509 , HOH A:601 , HOH A:602 , HOH A:623	BINDING SITE FOR RESIDUE MG A 506
7	AC7	SOFTWARE	ASP A:98 , ASP A:102 , MG A:506 , 0M7 A:509 , HOH A:603 , HOH A:604	BINDING SITE FOR RESIDUE MG A 507
8	AC8	SOFTWARE	ASP A:250 , 0M7 A:509 , HOH A:605 , HOH A:606 , HOH A:607	BINDING SITE FOR RESIDUE MG A 508
9	AC9	SOFTWARE	TYR A:94 , ASP A:98 , ASP A:102 , ARG A:107 , THR A:163 , GLN A:167 , LYS A:207 , TYR A:211 , ASP A:250 , LYS A:264 , IPE A:501 , MG A:506 , MG A:507 , MG A:508 , HOH A:603 , HOH A:604 , HOH A:605 , HOH A:606 , HOH A:607 , HOH A:623	BINDING SITE FOR RESIDUE 0M7 A 509

(no "SS Bond" information available for 4DWB)

(no "Cis Peptide Bond" information available for 4DWB)

(no "SAP(SNP)/Variant" information available for 4DWB)

(no "PROSITE Motif" information available for 4DWB)

(no "Exon" information available for 4DWB)

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:361
 aligned with Q95WL3_TRYCR | Q95WL3 from UniProtKB/TrEMBL  Length:362

    Alignment length:361
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360 
         Q95WL3_TRYCR     1 MASMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEKTHKRK 361
               SCOP domains d4dwba_ A: automated matches                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dwb A   1 MASMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEKTHKRK 361
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Terpenoid synthases (196)

Superfamily: Terpenoid synthases (196)

Family: automated matches (68)

Protein domain: automated matches (68)

Trypanosoma cruzi [TaxId: 5693] (14)

d4dwba_

(no "CATH Domain" information available for 4DWB)

(no "Pfam Domain" information available for 4DWB)

Asymmetric Unit(hide GO term definitions)

Chain A (Q95WL3_TRYCR | Q95WL3)

molecular function
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

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
		0M7	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		IPE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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
(no "Cis Peptide Bonds" information available for 4dwb)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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)

Access by PDB/NDB ID
	4dwb
		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
	Q95WL3_TRYCR \| Q95WL3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	2.5.1.10
		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
	Q95WL3_TRYCR \| Q95WL3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	Q95WL3_TRYCR \| Q95WL3	:	3id0
UniProtKB/TrEMBL
	Q95WL3_TRYCR \| Q95WL3	:	3iba 3ick 3icm 3icn 3icz 4dwg 4dxj 4dzw 4e1e

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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