4BY0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI CYP51 BOUND TO THE INHIBITOR (R)-N-(3-(1H-INDOL-3-YL)-1-OXO-1-(PYRIDIN-4-YLAMINO)PROPAN-2-YL)-3,3'-DIFLUORO-(1,1'-BIPHENYL)-4-CARBOXAMIDE

Authors :   J. Y. Choi, C. M. Calvet, D. F. Vieira, S. S. Gunatilleke, M. D. Cameron, J. H. Mckerrow, L. M. Podust, W. R. Roush

Date :   16 Jul 13 (Deposition) - 22 Jan 14 (Release) - 18 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Oxidoreductase, Sterol 14-Demethylase, Sterol Biosynthesis, Chagas Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Y. Choi, C. M. Calvet, D. F. Vieira, S. S. Gunatilleke, M. D. Cameron, J. H. Mckerrow, L. M. Podust, W. R. Roush
R-Configuration Of 4-Aminopyridyl-Based Inhibitors Of Cyp51 Confers Superior Efficacy Against Trypanosoma Cruzi
Acs Med. Chem. Lett. V. 5 434 2014
PubMed-ID: 24900854 | Reference-DOI: 10.1021/ML500010M

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(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 32-481
	Organism Scientific	:	TRYPANOSOMA CRUZI
	Organism Taxid	:	5693
	Other Details	:	32 N-TERMINUS RESIDUES ARE REPLACED WITH THE SEQUENCE MAKKTSSKGKL, 6XHIS TAG ENGINEERED AT THE C- TERMINUS
	Synonym	:	TC14DM, CYTOCHROME P450 51, LANOSTEROL 14-ALPHA DEMETHYLASE

		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	5PS	2	Ligand/Ion	(R)-N-(3-(1H-INDOL-3-YL)-1-OXO-1-(PYRIDIN-4-YLAMINO)PROPAN-2-YL)-3,3'-DIFLUORO-(1,1'-BIPHENYL)-4-CARBOXAMIDE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	5PS	1	Ligand/Ion	(R)-N-(3-(1H-INDOL-3-YL)-1-OXO-1-(PYRIDIN-4-YLAMINO)PROPAN-2-YL)-3,3'-DIFLUORO-(1,1'-BIPHENYL)-4-CARBOXAMIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	5PS	1	Ligand/Ion	(R)-N-(3-(1H-INDOL-3-YL)-1-OXO-1-(PYRIDIN-4-YLAMINO)PROPAN-2-YL)-3,3'-DIFLUORO-(1,1'-BIPHENYL)-4-CARBOXAMIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:103 , TYR A:116 , LEU A:127 , LEU A:130 , LEU A:134 , ALA A:288 , ALA A:291 , GLY A:292 , THR A:295 , SER A:296 , 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 , ILE A:423 , GLY A:424 , 5PS A:1460	BINDING SITE FOR RESIDUE HEM A1450
2	AC2	SOFTWARE	MET A:106 , TYR A:116 , VAL A:213 , ALA A:291 , LEU A:356 , MET A:358 , MET A:460 , VAL A:461 , HEM A:1450	BINDING SITE FOR RESIDUE 5PS A1460
3	AC3	SOFTWARE	TYR B:103 , TYR B:116 , ALA B:288 , ALA B:291 , GLY B:292 , THR B:295 , THR B:299 , VAL B:359 , ARG B:361 , GLY B:414 , PHE B:415 , GLY B:416 , HIS B:420 , CYS B:422 , GLY B:424 , 5PS B:1460	BINDING SITE FOR RESIDUE HEM B1450
4	AC4	SOFTWARE	TYR B:103 , MET B:106 , TYR B:116 , PHE B:290 , ALA B:291 , LEU B:356 , MET B:460 , HEM B:1450	BINDING SITE FOR RESIDUE 5PS B1460

(no "SS Bond" information available for 4BY0)

(no "Cis Peptide Bond" information available for 4BY0)

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 4BY0)

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:441
 aligned with CP51_TRYCC | Q7Z1V1 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:447
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       
           CP51_TRYCC    30 TDPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKEEASKDNNTSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRK 476
               SCOP domains d4by0a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhh.....eee....eeeee....hhhhhh......ee..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh------..hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhh.....eeeee...............eeeehhhhhh...................................hhhhhhhhhhhhhhhhhhhh.eee.......ee......ee.hhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------E------------------------------------------------------S------------------------------------------K---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME---------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4by0 A  30 KLPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKEE------TSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRK 476
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249 |     259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       
                                                                                                                                                                                                                                                       251    258

Chain B from PDB  Type:PROTEIN  Length:442
 aligned with CP51_TRYCC | Q7Z1V1 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:447
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       
           CP51_TRYCC    30 TDPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKEEASKDNNTSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRK 476
               SCOP domains d4by0b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhh....ee.......eee..hhhhhhhhhh.....ee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----..hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....eeeee...eee..eee....eeeehhhhhh............................hhhhh..hhhhhhhhhhhhhhhhhhheeeee.......ee......ee.hhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------E------------------------------------------------------S------------------------------------------K---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME---------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4by0 B  30 KLPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKEEA-----TSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRK 476
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249  |    259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       
                                                                                                                                                                                                                                                        252   258

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 Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome P450 (480)

Superfamily: Cytochrome P450 (480)

Family: automated matches (157)

Protein domain: automated matches (157)

Trypanosoma cruzi [TaxId: 5693] (5)

1a	d4by0a_	A:
1b	d4by0b_	B:

(no "CATH Domain" information available for 4BY0)

(no "Pfam Domain" information available for 4BY0)

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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Description

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (0, 0)

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