2VF6 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   HUMAN FDPS SYNTHASE IN COMPLEX WITH MINODRONATE

Authors :   A. G. Evdokimov, B. L. Barnett, F. H. Ebetino, M. Pokross

Date :   31 Oct 07 (Deposition) - 06 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Sgc, Structural Genomics, Structural Genomics Consortium, Trans-Prenyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Evdokimov, B. L. Barnett, F. H. Ebetino, M. Pokross
Human Fdps Synthase In Complex With Novel Inhibitor
To Be Published
PubMed: search

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHETASE
	Chains	:	A
	EC Number	:	2.5.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBR
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15 DERIVATIVE
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FPP SYNTHETASE, FPS, FARNESYL DIPHOSPHATE SYNTHETASE, DIMETHYLALLYLTRANSTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	M0N	1	Ligand/Ion	(1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
2	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	M0N	2	Ligand/Ion	(1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:99 , ASP A:103 , ASP A:107 , ARG A:112 , THR A:167 , GLN A:171 , LYS A:200 , THR A:201 , TYR A:204 , GLN A:240 , ASP A:243 , LYS A:257 , MG A:1352 , MG A:1353 , MG A:1354 , HOH A:2044 , HOH A:2049 , HOH A:2114 , HOH A:2117 , HOH A:2119 , HOH A:2122 , HOH A:2167 , HOH A:2168 , HOH A:2169 , HOH A:2170 , HOH A:2171	BINDING SITE FOR RESIDUE M0N A1351
2	AC2	SOFTWARE	ASP A:243 , M0N A:1351 , HOH A:2117 , HOH A:2119 , HOH A:2122	BINDING SITE FOR RESIDUE MG A1352
3	AC3	SOFTWARE	ASP A:103 , ASP A:107 , M0N A:1351 , MG A:1354 , HOH A:2044 , HOH A:2049	BINDING SITE FOR RESIDUE MG A1353
4	AC4	SOFTWARE	ASP A:103 , ASP A:107 , M0N A:1351 , MG A:1353 , HOH A:2050 , HOH A:2169 , HOH A:2170	BINDING SITE FOR RESIDUE MG A1354

(no "SS Bond" information available for 2VF6)

Asymmetric Unit

No.	Residues
1	Ala A:334	-	Pro A:335

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	113	Q
2	UniProt	VAR_061274	V	364	A	FPPS_HUMAN	Polymorphism	41314549	A	V	298	A
3	UniProt	VAR_049644	I	391	V	FPPS_HUMAN	Polymorphism	17456	A	I	325	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	113	Q
2	UniProt	VAR_061274	V	364	A	FPPS_HUMAN	Polymorphism	41314549	A	V	298	A
3	UniProt	VAR_049644	I	391	V	FPPS_HUMAN	Polymorphism	17456	A	I	325	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:100-114
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	FPPS_HUMAN	301-313	1	A:235-247

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:100-114
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	FPPS_HUMAN	301-313	2	A:235-247

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:9-47 (gaps)	39
1.3a	ENST00000368356	3a	ENSE00001054180	chr1:155282046-155282186	141	FPPS_HUMAN	114-160	47	1	A:48-94	47
1.4b	ENST00000368356	4b	ENSE00001054186	chr1:155287732-155287812	81	FPPS_HUMAN	161-187	27	1	A:95-121	27
1.5b	ENST00000368356	5b	ENSE00001054182	chr1:155287960-155288082	123	FPPS_HUMAN	188-228	41	1	A:122-162	41
1.5i	ENST00000368356	5i	ENSE00001054185	chr1:155288456-155288544	89	FPPS_HUMAN	229-258	30	1	A:163-192	30
1.5m	ENST00000368356	5m	ENSE00001054184	chr1:155288647-155288719	73	FPPS_HUMAN	258-282	25	1	A:192-216	25
1.6b	ENST00000368356	6b	ENSE00001054176	chr1:155289402-155289479	78	FPPS_HUMAN	283-308	26	1	A:217-242	26
1.6e	ENST00000368356	6e	ENSE00001054178	chr1:155289585-155289719	135	FPPS_HUMAN	309-353	45	1	A:243-287	45
1.7b	ENST00000368356	7b	ENSE00001939089	chr1:155290200-155290456	257	FPPS_HUMAN	354-419	66	1	A:288-350	63

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:337
 aligned with FPPS_HUMAN | P14324 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:342
                                    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  
           FPPS_HUMAN    75 VYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK 416
               SCOP domains d2vf6a_ A: automated m     atches                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2vf6A00 A:9-350 Farnes     yl Diphosphate Synthase                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains -----------------------------------polyprenyl_synt-2vf6A01 A:44-316                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh.-----..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A--------------------------V------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------POLYPRENYL_SYNT------------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1r  PDB: A:9-47 (gaps)          Exon 1.3a  PDB: A:48-94 UniProt: 114-160       Exon 1.4b  PDB: A:95-121   Exon 1.5b  PDB: A:122-162                Exon 1.5i  PDB: A:163-192     ------------------------Exon 1.6b  PDB: A:217-242 Exon 1.6e  PDB: A:243-287 UniProt: 309-353   Exon 1.7b  PDB: A:288-350 UniProt: 354-419 [INCOMPLETE]         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5m  PDB: A:192-216-------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2vf6 A   9 VYAQEKQDFVQHFSQIVRVLTE-----PEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK 350
                                    18        28 |     |38        48        58        68        78        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  
                                                30    36

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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: automated matches (68)

Protein domain: automated matches (68)

Human (Homo sapiens) [TaxId: 9606] (2)

d2vf6a_

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)

2vf6A00

A:9-350

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-2vf6A01

A:44-316

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:334 - Pro A:335	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	2vf6
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	FPPS_HUMAN \| P14324
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	2.5.1.1
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	616631
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1yq7	HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITHRISEDRONATE
1yv5	HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH MG ANDRISEDRONATE
1zw5	X-RAY STRUCTURE OF FARNESYL DIPHOSPHATE SYNTHASE PROTEIN
2f7m	CRYSTAL STRUCTURE OF UNLIGANDED HUMAN FPPS
2f89	CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH PAMIDRONATE
2f8c	CRYSTAL STRUCTURE OF FPPS IN COMPLEX WITH ZOLEDRONATE
2f8z	CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH ZOLEDRONATEAND ISOPENTENYL DIPHOSPHATE
2f92	CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH ALENDRONATE
2f94	CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH IBANDRONATE
2f9k	CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH ZOLEDRONATEAND ZN2+

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (2, 2)

Exons (9, 9)

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SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (17, 17)

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