1ZW5 - JenaLib

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Title :   X-RAY STRUCTURE OF FARNESYL DIPHOSPHATE SYNTHASE PROTEIN

Authors :   K. L. Kavanagh, K. Guo, X. Wu, F. Von Delft, C. Arrowsmith, M. Sundstrom A. Edwards, U. Oppermann, Structural Genomics Consortium (Sgc)

Date :   03 Jun 05 (Deposition) - 28 Jun 05 (Release) - 22 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Isoprenoid Pathway, Cholesterol Synthesis, Bisphosphonate, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. L. Kavanagh, K. Guo, J. E. Dunford, X. Wu, S. Knapp, F. H. Ebetino, M. J. Rogers, R. G. Russell, U. Oppermann
The Molecular Mechanism Of Nitrogen-Containing Bisphosphonates As Antiosteoporosis Drugs.
Proc. Natl. Acad. Sci. Usa V. 103 7829 2006
PubMed-ID: 16684881 | Reference-DOI: 10.1073/PNAS.0601643103

Molecule 1 - FARNESYL DIPHOSPHATE SYNTHASE
	Chains	:	A
	EC Number	:	2.5.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11 DERIVATIVE
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FDPS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FARNESYL PYROPHOSPHATE SYNTHETASE, DIMETHYLALLYL TRANSFERASE, GERANYL TRANSFERASE, FPPS, FDPS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2	MG	3	Ligand/Ion	MAGNESIUM ION
3	ZOL	1	Ligand/Ion	ZOLEDRONIC ACID

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	IPE	2	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZOL	2	Ligand/Ion	ZOLEDRONIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:117 , ASP A:121 , ZOL A:901 , MG A:909 , HOH A:911 , HOH A:913	BINDING SITE FOR RESIDUE MG A 907
2	AC2	SOFTWARE	ASP A:257 , ZOL A:901 , HOH A:915 , HOH A:917 , HOH A:960	BINDING SITE FOR RESIDUE MG A 908
3	AC3	SOFTWARE	ASP A:117 , ASP A:121 , ASP A:188 , ZOL A:901 , MG A:907 , HOH A:912 , HOH A:914 , HOH A:916	BINDING SITE FOR RESIDUE MG A 909
4	AC4	SOFTWARE	GLY A:70 , LYS A:71 , ARG A:74 , GLN A:110 , ARG A:127 , TYR A:218 , GLN A:254 , ASP A:257 , ZOL A:901 , HOH A:946 , HOH A:957 , HOH A:963 , HOH A:965 , HOH A:966 , HOH A:968	BINDING SITE FOR RESIDUE IPE A 900
5	AC5	SOFTWARE	ASP A:117 , ASP A:121 , ARG A:126 , LYS A:214 , THR A:215 , GLN A:254 , ASP A:257 , LYS A:271 , IPE A:900 , MG A:907 , MG A:908 , MG A:909 , HOH A:911 , HOH A:913 , HOH A:915 , HOH A:916 , HOH A:917 , HOH A:960 , HOH A:961	BINDING SITE FOR RESIDUE ZOL A 901

(no "SS Bond" information available for 1ZW5)

Asymmetric Unit

No.	Residues
1	Ala A:348	-	Pro A:349

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_075062	R	179	Q	FPPS_HUMAN	Disease (POROK9)	863225241	A	R	127	Q
2	UniProt	VAR_061274	V	364	A	FPPS_HUMAN	Polymorphism	41314549	A	V	312	A
3	UniProt	VAR_049644	I	391	V	FPPS_HUMAN	Polymorphism	17456	A	I	339	V

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

Biological Unit 1 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_075062	R	179	Q	FPPS_HUMAN	Disease (POROK9)	863225241	A	R	127	Q
2	UniProt	VAR_061274	V	364	A	FPPS_HUMAN	Polymorphism	41314549	A	V	312	A
3	UniProt	VAR_049644	I	391	V	FPPS_HUMAN	Polymorphism	17456	A	I	339	V

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	FPPS_HUMAN	166-180	1	A:114-128
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	FPPS_HUMAN	301-313	1	A:249-261

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	FPPS_HUMAN	166-180	2	A:114-128
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	FPPS_HUMAN	301-313	2	A:249-261

Asymmetric Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1e	ENST00000368356	1e	ENSE00001876084	chr1:155278643-155278756	114	FPPS_HUMAN	-	0	0	-	-
1.1q	ENST00000368356	1q	ENSE00001446957	chr1:155279580-155279756	177	FPPS_HUMAN	1-59	59	0	-	-
1.1r	ENST00000368356	1r	ENSE00001054179	chr1:155279834-155279996	163	FPPS_HUMAN	59-113	55	1	A:27-61 (gaps)	35
1.3a	ENST00000368356	3a	ENSE00001054180	chr1:155282046-155282186	141	FPPS_HUMAN	114-160	47	1	A:62-108	47
1.4b	ENST00000368356	4b	ENSE00001054186	chr1:155287732-155287812	81	FPPS_HUMAN	161-187	27	1	A:109-135	27
1.5b	ENST00000368356	5b	ENSE00001054182	chr1:155287960-155288082	123	FPPS_HUMAN	188-228	41	1	A:136-176	41
1.5i	ENST00000368356	5i	ENSE00001054185	chr1:155288456-155288544	89	FPPS_HUMAN	229-258	30	1	A:177-206	30
1.5m	ENST00000368356	5m	ENSE00001054184	chr1:155288647-155288719	73	FPPS_HUMAN	258-282	25	1	A:206-230	25
1.6b	ENST00000368356	6b	ENSE00001054176	chr1:155289402-155289479	78	FPPS_HUMAN	283-308	26	1	A:231-256	26
1.6e	ENST00000368356	6e	ENSE00001054178	chr1:155289585-155289719	135	FPPS_HUMAN	309-353	45	1	A:257-301	45
1.7b	ENST00000368356	7b	ENSE00001939089	chr1:155290200-155290456	257	FPPS_HUMAN	354-419	66	1	A:302-367	66

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:339
 aligned with FPPS_HUMAN | P14324 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:341
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418 
           FPPS_HUMAN    79 EKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK 419
               SCOP domains d1zw5a_ A: automated   matches                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1zw5A00 A:27-367 Far  nesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------polyprenyl_synt-1zw5A01 A:58-330                                                                                                                                                                                                                                                 ------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..--...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A--------------------------V---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------POLYPRENYL_SYNT------------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY---------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1r  PDB: A:27-61 (gaps)     Exon 1.3a  PDB: A:62-108 UniProt: 114-160      Exon 1.4b  PDB: A:109-135  Exon 1.5b  PDB: A:136-176                Exon 1.5i  PDB: A:177-206     ------------------------Exon 1.6b  PDB: A:231-256 Exon 1.6e  PDB: A:257-301 UniProt: 309-353   Exon 1.7b  PDB: A:302-367 UniProt: 354-419                         Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5m  PDB: A:206-230----------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1zw5 A  27 EKQDFVQHFSQIVRVLTEDE--HPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK 367
                                    36        46  |     56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366 
                                              46 49

Legend:		→ Mismatch	(orange background)
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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Terpenoid synthases (196)

Superfamily: Terpenoid synthases (196)

Family: Isoprenyl diphosphate synthases (57)

Protein domain: automated matches (38)

Human (Homo sapiens) [TaxId: 9606] (34)

d1zw5a_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Farnesyl Diphosphate Synthase (109)

Homologous Superfamily: Farnesyl Diphosphate Synthase (109)

Human (Homo sapiens) (18)

1zw5A00

A:27-367

Asymmetric Unit

Clans(

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Families(

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Organisms( (-)

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Clan: no clan defined [family: polyprenyl_synt] (86)

Family: polyprenyl_synt (86)

Homo sapiens (Human) (19)

polyprenyl_synt-1zw5A01

A:58-330

Asymmetric Unit(hide GO term definitions)

Chain A (FPPS_HUMAN | P14324)

molecular function
	GO:0004161	dimethylallyltranstransferase activity	Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate.
	GO:0004337	geranyltranstransferase activity	Catalysis of the reaction: geranyl diphosphate + isopentenyl diphosphate = 2-trans,6-trans-farnesyl diphosphate + diphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0006695	cholesterol biosynthetic process	The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
	GO:0008203	cholesterol metabolic process	The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
	GO:0045337	farnesyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of farnesyl diphosphate.
	GO:0033384	geranyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of geranyl diphosphate.
	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.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0006694	steroid biosynthetic process	The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	GO:0016126	sterol biosynthetic process	The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:348 - Pro A:349	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1zw5
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	FPPS_HUMAN \| P14324
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	2.5.1.10
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (9, 9)

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