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Asym./Biol. Unit (Jmol Viewer)

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Title :   T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPHOSPHONATE BPH-461 AND ISOPENTYL DIPHOSPHATE

Authors :   R. Cao, Y. Gao, H. Robinson, A. Goddard, E. Oldfield

Date :   27 Jul 08 (Deposition) - 05 May 09 (Release) - 05 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein-Bisphosphonate Complex, Isoprene Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhang, R. Cao, F. Yin, M. P. Hudock, R. T. Guo, K. Krysiak, S. Mukherjee, Y. G. Gao, H. Robinson, Y. Song, J. H. No, K. Bergan, A. Leon, L. Cass, A. Goddard, T. K. Chang, F. Y. Lin, E. Van Beek, S. Papapoulos, A. H. Wang, T. Kubo, M. Ochi, D. Mukkamala, E. Oldfield
Lipophilic Bisphosphonates As Dual Farnesyl/Geranylgeranyl Diphosphate Synthase Inhibitors: An X-Ray And Nmr Investigation.
J. Am. Chem. Soc. V. 131 5153 2009
PubMed-ID: 19309137 | Reference-DOI: 10.1021/JA808285E
(for further references see the PDB file header)

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	TRYPANOSOMA BRUCEI
	Organism Taxid	:	5691

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 13)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	IPR	2	Ligand/Ion	ISOPENTYL PYROPHOSPHATE
4	MG	6	Ligand/Ion	MAGNESIUM ION
5	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
6	NI9	2	Ligand/Ion	3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:103 , ASP A:107 , HOH A:5225	BINDING SITE FOR RESIDUE MG A 3002
02	AC2	SOFTWARE	ASP A:255 , HOH A:5001	BINDING SITE FOR RESIDUE MG A 3003
03	AC3	SOFTWARE	ASP A:103 , ASP A:107 , ASP A:175 , HOH A:5002 , HOH A:5003	BINDING SITE FOR RESIDUE MG A 3004
04	AC4	SOFTWARE	ASP B:103 , ASP B:107	BINDING SITE FOR RESIDUE MG B 4002
05	AC5	SOFTWARE	ASP B:255 , HOH B:5161 , HOH B:5264	BINDING SITE FOR RESIDUE MG B 4003
06	AC6	SOFTWARE	ASP B:103 , ASP B:107 , ASP B:175 , HOH B:5004	BINDING SITE FOR RESIDUE MG B 4004
07	AC7	SOFTWARE	TYR A:99 , ASP A:103 , ASP A:107 , ARG A:112 , GLN A:172 , LYS A:212 , THR A:213 , TYR A:216 , GLN A:252 , ASP A:255 , LYS A:269 , HOH A:5001 , HOH A:5003 , HOH A:5060 , HOH A:5143 , HOH A:5225	BINDING SITE FOR RESIDUE NI9 A 3001
08	AC8	SOFTWARE	TYR B:99 , ASP B:103 , ASP B:107 , ARG B:112 , GLN B:172 , LYS B:212 , THR B:213 , ASP B:255 , LYS B:269 , HOH B:5004 , HOH B:5116 , HOH B:5117 , HOH B:5161	BINDING SITE FOR RESIDUE NI9 B 4001
09	AC9	SOFTWARE	CYS B:159 , ARG B:160 , ARG B:163	BINDING SITE FOR RESIDUE BME B 9001
10	BC1	SOFTWARE	LYS B:47 , ARG B:50 , GLN B:96 , ARG B:113 , TYR B:216 , PHE B:251 , GLN B:252 , ASP B:255 , ARG B:365 , HOH B:5045 , HOH B:5112 , HOH B:5275	BINDING SITE FOR RESIDUE IPR B 6002
11	BC2	SOFTWARE	GLY A:46 , LYS A:47 , ARG A:50 , GLN A:96 , ARG A:113 , TYR A:216 , THR A:217 , PHE A:251 , GLN A:252 , ASP A:255 , HOH A:5006 , HOH A:5022 , HOH A:5149 , HOH A:5151 , HOH A:5242 , HOH A:5252	BINDING SITE FOR RESIDUE IPR A 6001
12	BC3	SOFTWARE	ARG A:163 , THR A:167 , TYR A:215 , HOH A:5294 , LYS B:24	BINDING SITE FOR RESIDUE MPD A 7001

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

(no "Cis Peptide Bond" information available for 3DYF)

(no "SAP(SNP)/Variant" information available for 3DYF)

(no "PROSITE Motif" information available for 3DYF)

(no "Exon" information available for 3DYF)

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:357
 aligned with Q86C09_9TRYP | Q86C09 from UniProtKB/TrEMBL  Length:367

    Alignment length:367
                                    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       
         Q86C09_9TRYP     1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
               SCOP domains d3dyfa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3dyfA00 A:1-367 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..----------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dyf A   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLS----------DGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
                                    10        20        30        40        50        60  |      -   |    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       
                                                                                         63         74

Chain B from PDB  Type:PROTEIN  Length:358
 aligned with Q86C09_9TRYP | Q86C09 from UniProtKB/TrEMBL  Length:367

    Alignment length:367
                                    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       
         Q86C09_9TRYP     1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
               SCOP domains d3dyfb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3dyfB00 B:1-367 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dyf B   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSL---------DGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
                                    10        20        30        40        50        60   |     -   |    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       
                                                                                          64        74

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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Terpenoid synthases (196)

Superfamily: Terpenoid synthases (196)

Family: automated matches (68)

Protein domain: automated matches (68)

Trypanosome (Trypanosoma brucei) [TaxId: 5691] (9)

1a	d3dyfa_	A:
1b	d3dyfb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Farnesyl Diphosphate Synthase (109)

Homologous Superfamily: Farnesyl Diphosphate Synthase (109)

Trypanosoma brucei. Organism_taxid: 5691. (9)

1a	3dyfA00	A:1-367
1b	3dyfB00	B:1-367

(no "Pfam Domain" information available for 3DYF)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q86C09_9TRYP | Q86C09)

molecular function
	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: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/Biological Unit
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	Cis Peptide Bonds
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	3dyf
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Description

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Chains, Units

Ligands, Modified Residues, Ions (6, 13)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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