4K10 - JenaLib

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Title :   CRYSTAL STRUCTURE OF LESHMANIASIS MAJOR FARNESYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM AND MG2+

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

Date :   04 Apr 13 (Deposition) - 02 Apr 14 (Release) - 02 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Geranyl Transferase, Fpps, Farnesyl Pyrophosphate Synthase, Farnesyl Diphosphate Synthase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Aripirala, D. Gonzalez-Pacanowska, E. Oldfield, M. Kaiser, L. M. Amzel, S. B. Gabelli
Structural And Thermodynamic Basis Of The Inhibition Of Leishmania Major Farnesyl Diphosphate Synthase By Nitrogen-Containing Bisphosphonates.
Acta Crystallogr. , Sect. D V. 70 802 2014
PubMed-ID: 24598749 | Reference-DOI: 10.1107/S1399004713033221

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
	Chains	:	A, B, D, C
	EC Number	:	2.5.1.1, 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, LMJF_22_1360
	Organism Scientific	:	LEISHMANIA MAJOR
	Organism Taxid	:	5664

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 22)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	MG	8	Ligand/Ion	MAGNESIUM ION
4	NA	6	Ligand/Ion	SODIUM ION
5	NI9	4	Ligand/Ion	3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM
6	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	NI9	2	Ligand/Ion	3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM
6	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	NI9	2	Ligand/Ion	3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM
6	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:531 , HOH B:555	BINDING SITE FOR RESIDUE NA A 401
02	AC2	SOFTWARE	HIS A:157 , ASP A:160 , HOH A:521 , ALA B:133 , HOH B:509	BINDING SITE FOR RESIDUE NA A 402
03	AC3	SOFTWARE	HOH B:538	BINDING SITE FOR RESIDUE NA A 403
04	AC4	SOFTWARE	ASP A:250 , NI9 A:406 , HOH A:503 , HOH A:510 , HOH A:511 , HOH A:512 , HOH A:560	BINDING SITE FOR RESIDUE MG A 404
05	AC5	SOFTWARE	ASP A:98 , ASP A:102 , NI9 A:406 , HOH A:517	BINDING SITE FOR RESIDUE MG A 405
06	AC6	SOFTWARE	LEU A:95 , ASP A:98 , ARG A:107 , GLN A:167 , LYS A:207 , TYR A:211 , LYS A:273 , MG A:404 , MG A:405 , HOH A:503 , HOH A:560 , HOH A:563	BINDING SITE FOR RESIDUE NI9 A 406
07	AC7	SOFTWARE	ALA A:133 , HOH A:527 , HIS B:157 , ASP B:160	BINDING SITE FOR RESIDUE NA B 401
08	AC8	SOFTWARE	LYS A:233 , HIS A:236 , VAL D:30 , LYS D:33 , GLY D:34 , LYS D:37	BINDING SITE FOR RESIDUE PEG A 407
09	AC9	SOFTWARE	LYS B:48 , TYR B:49 , GLN B:91 , HOH B:529	BINDING SITE FOR RESIDUE ACT B 402
10	BC1	SOFTWARE	ASP B:250 , LYS B:273 , HOH B:503 , HOH B:507	BINDING SITE FOR RESIDUE MG B 403
11	BC2	SOFTWARE	ASP B:98 , ASP B:102 , NI9 B:405 , HOH B:558 , HOH B:560	BINDING SITE FOR RESIDUE MG B 404
12	BC3	SOFTWARE	ASP B:98 , GLN B:167 , ASP B:170 , LYS B:207 , TYR B:211 , MG B:404 , HOH B:502 , HOH B:507 , HOH B:560 , HOH B:570	BINDING SITE FOR RESIDUE NI9 B 405
13	BC4	SOFTWARE	ARG C:154 , ASP C:158 , HIS D:141 , ALA D:144 , HOH D:506 , HOH D:541	BINDING SITE FOR RESIDUE MES D 401
14	BC5	SOFTWARE	ALA D:2 , HIS D:3 , GLU D:60 , LYS D:64	BINDING SITE FOR RESIDUE ACT D 402
15	BC6	SOFTWARE	ASP D:250 , HOH D:501 , HOH D:502 , HOH D:503 , HOH D:517	BINDING SITE FOR RESIDUE MG D 403
16	BC7	SOFTWARE	ASP D:98 , ASP D:102 , NI9 D:405 , HOH D:504 , HOH D:551 , HOH D:553	BINDING SITE FOR RESIDUE MG D 404
17	BC8	SOFTWARE	ASP D:98 , ARG D:107 , GLN D:167 , LYS D:207 , TYR D:211 , MG D:404 , HOH D:502 , HOH D:504 , HOH D:554 , HOH D:558	BINDING SITE FOR RESIDUE NI9 D 405
18	BC9	SOFTWARE	HIS C:157 , ASP C:160 , HOH C:501 , ALA D:133 , HOH D:507	BINDING SITE FOR RESIDUE NA C 401
19	CC1	SOFTWARE	ASP C:250 , NI9 C:405 , HOH C:504 , HOH C:505 , HOH C:563 , HOH C:570	BINDING SITE FOR RESIDUE MG C 403
20	CC2	SOFTWARE	ASP C:98 , ASP C:102 , NI9 C:405 , HOH C:561	BINDING SITE FOR RESIDUE MG C 404
21	CC3	SOFTWARE	PHE C:94 , LEU C:95 , ASP C:98 , ARG C:107 , GLN C:167 , LYS C:207 , TYR C:211 , LYS C:273 , MG C:403 , MG C:404 , HOH C:533 , HOH C:561 , HOH C:571	BINDING SITE FOR RESIDUE NI9 C 405

(no "SS Bond" information available for 4K10)

Asymmetric Unit

No.	Residues
1	Pro A:258	-	Pro A:259
2	Met B:1	-	Ala B:2

(no "SAP(SNP)/Variant" information available for 4K10)

(no "PROSITE Motif" information available for 4K10)

(no "Exon" information available for 4K10)

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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4k10a_ A: automated matches                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k10 A   1 MAHMERFQKVYEEVQEFLLGDAEKRFEMDVHRKGYLKSMMDTTCLGGKYNRGLCVVDVAEAMAKDTQMDAAAMERVLHDACVCGWMIEMLQAHFLVEDDIMDHSKTRRGKPCWYLHPGVTAQVAINDGLILLAWATQMALHYFADRPFLAEVLRVFHDVDLTTTIGQLYDVTSMVDSAKLDAKVAHANTTDYVEYTPFNHRRIVVYKTAYYTYWLPLVMGLLVSGTLEKVDKKATHKVAMVMGEYFQVQDDVMDCFTPPEKIGTDIEDAKCSWLAVTFLTTAPAEKVAEFKANYGSTDPAAVAVIKQLYTEQNLLARFEEYEKAVVAEVEQLIAALEAQNAAFAASVKVLWSKTYKRQ 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|      273       283       293       303       313       323       333       343       353        
                                                                                                                                                                                                                                                                                             260|                                                                                                 
                                                                                                                                                                                                                                                                                              264

Chain B from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4k10b_ B: automated matches                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k10 B   1 MAHMERFQKVYEEVQEFLLGDAEKRFEMDVHRKGYLKSMMDTTCLGGKYNRGLCVVDVAEAMAKDTQMDAAAMERVLHDACVCGWMIEMLQAHFLVEDDIMDHSKTRRGKPCWYLHPGVTAQVAINDGLILLAWATQMALHYFADRPFLAEVLRVFHDVDLTTTIGQLYDVTSMVDSAKLDAKVAHANTTDYVEYTPFNHRRIVVYKTAYYTYWLPLVMGLLVSGTLEKVDKKATHKVAMVMGEYFQVQDDVMDCFTPPEKLGKIGTDIEDAKCSWLAVTFLTTAPAEKVAEFKANYGSTDPAAVAVIKQLYTEQNLLARFEEYEKAVVAEVEQLIAALEAQNAAFAASVKVLWSKTY 358
                                    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

Chain C from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4k10c_ C: automated matches                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k10 C   1 MAHMERFQKVYEEVQEFLLGDAEKRFEMDVHRKGYLKSMMDTTCLGGKYNRGLCVVDVAEAMAKDTQMDAAAMERVLHDACVCGWMIEMLQAHFLVEDDIMDHSKTRRGKPCWYLHPGVTAQVAINDGLILLAWATQMALHYFADRPFLAEVLRVFHDVDLTTTIGQLYDVTSMVDSAKLDAKVAHANTTDYVEYTPFNHRRIVVYKTAYYTYWLPLVMGLLVSGTLEKVDKKATHKVAMVMGEYFQVQDDVMDCFTPPEKGKIGTDIEDAKCSWLAVTFLTTAPAEKVAEFKANYGSTDPAAVAVIKQLYTEQNLLARFEEYEKAVVAEVEQLIAALEAQNAAFAASVKVLWSKTYKRQ 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||     271       281       291       301       311       321       331       341       351       361
                                                                                                                                                                                                                                                                                              261|                                                                                                  
                                                                                                                                                                                                                                                                                               263

Chain D from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4k10d_ D: automated matches                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k10 D   1 MAHMERFQKVYEEVQEFLLGDAEKRFEMDVHRKGYLKSMMDTTCLGGKYNRGLCVVDVAEAMAKDTQMDAAAMERVLHDACVCGWMIEMLQAHFLVEDDIMDHSKTRRGKPCWYLHPGVTAQVAINDGLILLAWATQMALHYFADRPFLAEVLRVFHDVDLTTTIGQLYDVTSMVDSAKLDAKVAHANTTDYVEYTPFNHRRIVVYKTAYYTYWLPLVMGLLVSGTLEKVDKKATHKVAMVMGEYFQVQDDVMDCFTPPEKLGKIGTDIEDAKCSWLAVTFLTTAPAEKVAEFKANYGSTDPAAVAVIKQLYTEQNLLARFEEYEKAVVAEVEQLIAALEAQNAAFAASVKVLWSKTYKR 360
                                    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

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	-	→ 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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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)

Leishmania major [TaxId: 5664] (3)

1a	d4k10a_	A:
1b	d4k10b_	B:
1c	d4k10c_	C:
1d	d4k10d_	D:

(no "CATH Domain" information available for 4K10)

(no "Pfam Domain" information available for 4K10)

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	Cis Peptide Bonds
		Met B:1 - Ala B:2	[ RasMol ]
		Pro A:258 - Pro A:259	[ RasMol ]

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	Q4QBL1_LEIMA \| Q4QBL1	:	4jzb 4jzx

4jzb	LMFPPS IN COMPLEX WITH 30OB, IPP AND CA2+
4jzx

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 22)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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