4CK8 - JenaLib

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Title :   STEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMPLEX WITH (R)-1-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YL)ETHYL 4-(4-(3,4-DICHLOROPHENYL)PIPERAZIN-1-YL)PHENYLCARBAMATE (LFD)

Authors :   L. Friggeri, Z. Wawrzak, S. Tortorella, G. I. Lepesheva

Date :   30 Dec 13 (Deposition) - 30 Jul 14 (Release) - 27 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.62

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

Keywords :   Cytochrome P450, Oxidoreductase, Monooxygenase, Sterol Biosynthesis, Eukaryotic Membranes, Cytochrome P450 Fold, Endoplasmic Reticulum Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Friggeri, T. Y. Hargrove, G. Rachakonda, A. D. Williams, Z. Wawrzak R. Di Santo, D. De Vita, M. R. Waterman, S. Tortorella, F. Villalta, G. I. Lepesheva
Structural Basis For Rational Design Of Inhibitors Targeting Trypanosoma Cruzi Sterol 14Alpha-Demethylase: Two Regions Of The Enzyme Molecule Potentiate Its Inhibition.
J. Med. Chem. V. 57 6704 2014
PubMed-ID: 25033013 | Reference-DOI: 10.1021/JM500739F

Molecule 1 - STEROL 14-ALPHA DEMETHYLASE
	Chains	:	A, B
	EC Number	:	1.14.13.70
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCW
	Expression System Strain	:	HMS174
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 32-481
	Organism Scientific	:	TRYPANOSOMA CRUZI
	Organism Taxid	:	5693
	Other Details	:	GENBANK AAW47718.1
	Strain	:	THLAHUEN
	Synonym	:	TC14DM, CYTOCHROME P450 51, CYP51

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	LFD	2	Ligand/Ion	(1R)-1-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YL)ETHYL {4-[4-(3,4-DICHLOROPHENYL)PIPERAZIN-1-YL]PHENYL}CARBAMATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	LFD	1	Ligand/Ion	(1R)-1-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YL)ETHYL {4-[4-(3,4-DICHLOROPHENYL)PIPERAZIN-1-YL]PHENYL}CARBAMATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	LFD	1	Ligand/Ion	(1R)-1-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YL)ETHYL {4-[4-(3,4-DICHLOROPHENYL)PIPERAZIN-1-YL]PHENYL}CARBAMATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:103 , ALA A:288 , ALA A:291 , GLY A:292 , THR A:295 , THR A:299 , LEU A:356 , VAL A:359 , ARG A:361 , GLY A:414 , PHE A:415 , GLY A:416 , HIS A:420 , LYS A:421 , CYS A:422 , GLY A:424 , LFD A:1490	BINDING SITE FOR RESIDUE HEM A1480
2	AC2	SOFTWARE	ILE A:45 , PHE A:48 , PHE A:110 , TYR A:116 , PRO A:210 , VAL A:213 , PHE A:290 , ALA A:291 , THR A:295 , MET A:460 , HEM A:1480	BINDING SITE FOR RESIDUE LFD A1490
3	AC3	SOFTWARE	TYR B:103 , ARG B:124 , LEU B:127 , ALA B:288 , ALA B:291 , GLY B:292 , THR B:295 , THR B:299 , LEU B:356 , VAL B:359 , ARG B:361 , GLY B:414 , PHE B:415 , GLY B:416 , HIS B:420 , CYS B:422 , ILE B:423 , GLY B:424 , LFD B:1490	BINDING SITE FOR RESIDUE HEM B1480
4	AC4	SOFTWARE	ILE B:45 , GLY B:49 , TYR B:103 , PHE B:110 , TYR B:116 , PRO B:210 , PHE B:290 , ALA B:291 , THR B:295 , LEU B:356 , MET B:460 , HEM B:1480	BINDING SITE FOR RESIDUE LFD B1490

(no "SS Bond" information available for 4CK8)

Asymmetric Unit

No.	Residues
1	Arg B:220	-	Leu B:221

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CP51_TRYCC_001 *	D	62	E	CP51_TRYCC	---	---	A/B	D	62	E
2	UniProt	VAR_CP51_TRYCC_002 *	A	117	S	CP51_TRYCC	---	---	A/B	A	117	S
3	UniProt	VAR_CP51_TRYCC_003 *	E	160	K	CP51_TRYCC	---	---	A/B	E	160	K
	* ID not provided by source

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CP51_TRYCC_001 *	D	62	E	CP51_TRYCC	---	---	A	D	62	E
2	UniProt	VAR_CP51_TRYCC_002 *	A	117	S	CP51_TRYCC	---	---	A	A	117	S
3	UniProt	VAR_CP51_TRYCC_003 *	E	160	K	CP51_TRYCC	---	---	A	E	160	K
	* ID not provided by source

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CP51_TRYCC_001 *	D	62	E	CP51_TRYCC	---	---	B	D	62	E
2	UniProt	VAR_CP51_TRYCC_002 *	A	117	S	CP51_TRYCC	---	---	B	A	117	S
3	UniProt	VAR_CP51_TRYCC_003 *	E	160	K	CP51_TRYCC	---	---	B	E	160	K
	* ID not provided by source

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP51_TRYCC	415-424	2	A:415-424 B:415-424

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP51_TRYCC	415-424	1	A:415-424 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP51_TRYCC	415-424	1	- B:415-424

(no "Exon" information available for 4CK8)

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:449
 aligned with CP51_TRYCC | Q7Z1V1 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:450
                                    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       358       368       378       388       398       408       418       428       438       448       458       468       478
           CP51_TRYCC    29 PTDPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKEEASKDNNTSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRKKK 478
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.hhhhhhhhhh.....ee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.-..hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhh.....eeeee...eee..eee....eeeehhhhhh............................hhhhh..hhhhhhhhhhhhhhhhhhhee..........ee......ee.hhh.eee.ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------E------------------------------------------------------S------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ck8 A  29 KKTPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRL-LPQSARCREARAELQKILGEIIVAREKEEASKDNNTSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRKKK 478
                                    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       358       368       378       388       398       408       418       428       438       448       458       468       478
                                                                                                                                                                                                                          221 |                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                            223

Chain B from PDB  Type:PROTEIN  Length:450
 aligned with CP51_TRYCC | Q7Z1V1 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:451
                                    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       357       367       377       387       397       407       417       427       437       447       457       467       477 
           CP51_TRYCC    28 RPTDPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKEEASKDNNTSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRKKK 478
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.hhhhhhhhhh.....ee.hhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhh.-..hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhh.....eeeee...eee..eee....eeeehhhhhh............................hhhhh..hhhhhhhhhhhhhhhhhhhee..........ee......ee.hhh.eee.ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------E------------------------------------------------------S------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ck8 B  28 AKKTPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRL-LPQSARCREARAELQKILGEIIVAREKEEASKDNNTSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRKKK 478
                                    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       357       367       377       387       397       407       417       427       437       447       457       467       477 
                                                                                                                                                                                                                           221 |                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                             223

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 '\|'

(no "SCOP Domain" information available for 4CK8)

(no "CATH Domain" information available for 4CK8)

(no "Pfam Domain" information available for 4CK8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CP51_TRYCC | Q7Z1V1)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
	GO:0008398	sterol 14-demethylase activity	Catalysis of the reaction: obtusifoliol + 3 O2 + 3 NADPH + 3 H+ = 4-alpha-methyl-5-alpha-ergosta-8,14,24(28)-trien-3-beta-ol + formate + 3 NADP+ + 3 H2O.
biological process
	GO:0070988	demethylation	The process of removing one or more methyl groups from a molecule.
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	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.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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4ck9	STEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMPLEX WITH (S)-1-(4-CHLOROPHENYL)-2-(1H- IMIDAZOL-1-YL)ETHYL 4-ISOPROPYLPHENYLCARBAMATE (LFT)
4cka	STEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMPLEX WITH (S)-1-(4-FLUOROPHENYL)-2-(1H- IMIDAZOL-1-YL)ETHYL 4-ISOPROPYLPHENYLCARBAMATE (LFS)

Description

Compounds

Structural Features

Chains, Units

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, 6)

PROSITE Motifs (1, 2)

Exons (0, 0)

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