3N45 - JenaLib

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Title :   HUMAN FPPS COMPLEX WITH FBS_04 AND ZOLEDRONIC ACID/MG2+

Authors :   J. -M. Rondeau

Date :   21 May 10 (Deposition) - 18 Aug 10 (Release) - 01 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

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

Keywords :   Bisphosphonate; Fragment-Based Screening; Transferase; Isoprene Biosynthesis; Cholesterol Biosynthesis, Transferase, Transferase- Transferase Inhibiator Complex, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Jahnke, J. M. Rondeau, S. Cotesta, A. Marzinzik, X. Pelle, M. Geiser A. Strauss, M. Gotte, F. Bitsch, R. Hemmig, C. Henry, S. Lehmann, J. F. Glickman, T. P. Roddy, S. J. Stout, J. R. Green
Allosteric Non-Bisphosphonate Fpps Inhibitors Identified By Fragment-Based Discovery.
Nat. Chem. Biol. V. 6 660 2010
PubMed-ID: 20711197 | Reference-DOI: 10.1038/NCHEMBIO.421
(for further references see the PDB file header)

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
	Chains	:	F
	EC Number	:	2.5.1.1, 2.5.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21 TUNER (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 72-419
	Gene	:	FDPS, FPS, KIAA1293
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FPP SYNTHASE, FPS, FARNESYL DIPHOSPHATE SYNTHASE, DIMETHYLALLYLTRANSTRANSFERASE, GERANYLTRANSTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	3N3	1	Ligand/Ion	(2S)-1-[(BENZYLOXY)CARBONYL]-2,3-DIHYDRO-1H-INDOLE-2-CARBOXYLIC ACID
2	MG	3	Ligand/Ion	MAGNESIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	ZOL	1	Ligand/Ion	ZOLEDRONIC ACID

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	3N3	2	Ligand/Ion	(2S)-1-[(BENZYLOXY)CARBONYL]-2,3-DIHYDRO-1H-INDOLE-2-CARBOXYLIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PO4	4	Ligand/Ion	PHOSPHATE ION
4	ZOL	2	Ligand/Ion	ZOLEDRONIC ACID

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS F:57 , ASN F:59 , ARG F:60 , SER F:205 , PHE F:206 , PHE F:239 , GLN F:242 , LEU F:246 , LEU F:344 , LYS F:347 , ILE F:348 , PO4 F:356 , HOH F:484	BINDING SITE FOR RESIDUE 3N3 F 1
2	AC2	SOFTWARE	MG F:2 , MG F:3 , ASP F:103 , ASP F:107 , ARG F:112 , GLN F:171 , LYS F:200 , THR F:201 , GLN F:240 , ASP F:243 , LYS F:257 , MG F:355 , PO4 F:357 , HOH F:358 , HOH F:360 , HOH F:361 , HOH F:363 , HOH F:364 , HOH F:365 , HOH F:366 , HOH F:373 , HOH F:374 , HOH F:379	BINDING SITE FOR RESIDUE ZOL F 354
3	AC3	SOFTWARE	MG F:3 , ASP F:103 , ASP F:107 , ZOL F:354 , HOH F:358 , HOH F:361	BINDING SITE FOR RESIDUE MG F 355
4	AC4	SOFTWARE	ASP F:243 , ZOL F:354 , HOH F:363 , HOH F:365 , HOH F:374	BINDING SITE FOR RESIDUE MG F 2
5	AC5	SOFTWARE	ASP F:103 , ASP F:107 , ZOL F:354 , MG F:355 , HOH F:359 , HOH F:360 , HOH F:364	BINDING SITE FOR RESIDUE MG F 3
6	AC6	SOFTWARE	3N3 F:1 , GLY F:56 , LYS F:57 , ARG F:60 , GLN F:96 , ARG F:113 , PO4 F:357 , HOH F:382 , HOH F:420 , HOH F:442 , HOH F:484	BINDING SITE FOR RESIDUE PO4 F 356
7	AC7	SOFTWARE	ARG F:60 , GLN F:96 , ARG F:112 , PHE F:239 , LYS F:257 , ZOL F:354 , PO4 F:356 , HOH F:382 , HOH F:392	BINDING SITE FOR RESIDUE PO4 F 357

(no "SS Bond" information available for 3N45)

Asymmetric Unit

No.	Residues
1	Ala F:334	-	Pro F: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	F	R	113	Q
2	UniProt	VAR_061274	V	364	A	FPPS_HUMAN	Polymorphism	41314549	F	V	298	A
3	UniProt	VAR_049644	I	391	V	FPPS_HUMAN	Polymorphism	17456	F	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	F	R	113	Q
2	UniProt	VAR_061274	V	364	A	FPPS_HUMAN	Polymorphism	41314549	F	V	298	A
3	UniProt	VAR_049644	I	391	V	FPPS_HUMAN	Polymorphism	17456	F	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	F:100-114
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	FPPS_HUMAN	301-313	1	F: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	F:100-114
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	FPPS_HUMAN	301-313	2	F: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	F:8-47	40
1.3a	ENST00000368356	3a	ENSE00001054180	chr1:155282046-155282186	141	FPPS_HUMAN	114-160	47	1	F:48-94	47
1.4b	ENST00000368356	4b	ENSE00001054186	chr1:155287732-155287812	81	FPPS_HUMAN	161-187	27	1	F:95-121	27
1.5b	ENST00000368356	5b	ENSE00001054182	chr1:155287960-155288082	123	FPPS_HUMAN	188-228	41	1	F:122-162	41
1.5i	ENST00000368356	5i	ENSE00001054185	chr1:155288456-155288544	89	FPPS_HUMAN	229-258	30	1	F:163-192	30
1.5m	ENST00000368356	5m	ENSE00001054184	chr1:155288647-155288719	73	FPPS_HUMAN	258-282	25	1	F:192-216	25
1.6b	ENST00000368356	6b	ENSE00001054176	chr1:155289402-155289479	78	FPPS_HUMAN	283-308	26	1	F:217-242	26
1.6e	ENST00000368356	6e	ENSE00001054178	chr1:155289585-155289719	135	FPPS_HUMAN	309-353	45	1	F:243-287	45
1.7b	ENST00000368356	7b	ENSE00001939089	chr1:155290200-155290456	257	FPPS_HUMAN	354-419	66	1	F: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
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Chain F from PDB  Type:PROTEIN  Length:343
 aligned with FPPS_HUMAN | P14324 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:343
                                    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   
           FPPS_HUMAN    74 DVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK 416
               SCOP domains d3n45f_ F: automated matches                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------polyprenyl_synt-3n45F01 F:44-316                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A--------------------------V------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------POLYPRENYL_SYNT------------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1r  PDB: F:8-47 UniProt: 59-113  Exon 1.3a  PDB: F:48-94 UniProt: 114-160       Exon 1.4b  PDB: F:95-121   Exon 1.5b  PDB: F:122-162                Exon 1.5i  PDB: F:163-192     ------------------------Exon 1.6b  PDB: F:217-242 Exon 1.6e  PDB: F:243-287 UniProt: 309-353   Exon 1.7b  PDB: F:288-350 UniProt: 354-419 [INCOMPLETE]         Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5m  PDB: F:192-216-------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3n45 F   8 DVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK 350
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347

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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)

d3n45f_

(no "CATH Domain" information available for 3N45)

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-3n45F01

F:44-316

Asymmetric Unit(hide GO term definitions)

Chain F (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.

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	Cis Peptide Bonds
		Ala F:334 - Pro F:335	[ RasMol ]

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	3n45
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	616631
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3n1v	HUMAN FPPS COMPLEX WITH FBS_01
3n1w	HUMAN FPPS COMPLEX WITH FBS_02
3n3l	HUMAN FPPS COMPLEX WITH FBS_03
3n46	HUMAN FPPS COMPLEX WITH NOV_980 AND ZOLEDRONIC ACID/MG2+
3n49	HUMAN FPPS COMPLEX WITH NOV_982
3n5h	HUMAN FPPS COMPLEX WITH NOV_304
3n5j	HUMAN FPPS COMPLEX WITH NOV_311
3n6k	HUMAN FPPS COMPLEX WITH NOV_823

Description

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Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

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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