4COH - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI CYP51 BOUND TO THE SULFONAMIDE DERIVATIVE OF THE 4-AMINOPYRIDYL-BASED INHIBITOR

Authors :   D. F. Vieira, J. Y. Choi, W. R. Roush, L. M. Podust

Date :   28 Jan 14 (Deposition) - 02 Apr 14 (Release) - 04 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.08

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

Keywords :   Transferase, Cyp51, Sterol 14-Demethylase, Sterol Biosynthesis, Chagas Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. F. Vieira, J. Y. Choi, W. R. Roush, L. M. Podust
Expanding The Binding Envelope Of Cyp51 Inhibitors Targeting Trypanosoma Cruzi With 4-Aminopyridyl-Based Sulfonamide Derivatives
Chembiochem V. 15 1111 2014
PubMed-ID: 24771705 | Reference-DOI: 10.1002/CBIC.201402027

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 29-481
	Organism Scientific	:	TRYPANOSOMA CRUZI
	Organism Taxid	:	5693
	Synonym	:	TC14DM, CYTOCHROME P450 51, LANOSTEROL 14-ALPHA DEMETHYLASE , STEROL 14-DEMETHYLASE, 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	T9H	2	Ligand/Ion	2-FLUORANYL-N-[(2R)-3-(1H-INDOL-3-YL)-1-OXIDANYLIDENE-1-(PYRIDIN-4-YLAMINO)PROPAN-2-YL]-4-(4-THIOPHEN-2-YLSULFONYLPIPERAZIN-1-YL)BENZAMIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	T9H	1	Ligand/Ion	2-FLUORANYL-N-[(2R)-3-(1H-INDOL-3-YL)-1-OXIDANYLIDENE-1-(PYRIDIN-4-YLAMINO)PROPAN-2-YL]-4-(4-THIOPHEN-2-YLSULFONYLPIPERAZIN-1-YL)BENZAMIDE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	T9H	1	Ligand/Ion	2-FLUORANYL-N-[(2R)-3-(1H-INDOL-3-YL)-1-OXIDANYLIDENE-1-(PYRIDIN-4-YLAMINO)PROPAN-2-YL]-4-(4-THIOPHEN-2-YLSULFONYLPIPERAZIN-1-YL)BENZAMIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:116 , 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 , CYS A:422 , ILE A:423 , GLY A:424 , T9H A:1460 , HOH A:2076 , HOH A:2307 , HOH A:2310 , HOH A:2362	BINDING SITE FOR RESIDUE HEM A1450
2	AC2	SOFTWARE	PHE A:48 , TYR A:103 , MET A:106 , PHE A:110 , TYR A:116 , PRO A:210 , ALA A:211 , PHE A:214 , ALA A:291 , LEU A:356 , MET A:460 , VAL A:461 , HEM A:1450 , HOH A:2011 , HOH A:2225 , HOH A:2363	BINDING SITE FOR RESIDUE T9H A1460
3	AC3	SOFTWARE	TYR B:116 , LEU B:134 , ALA B:288 , ALA B:291 , THR B:295 , 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 , T9H B:1460 , HOH B:2088 , HOH B:2278 , HOH B:2313	BINDING SITE FOR RESIDUE HEM B1450
4	AC4	SOFTWARE	PRO A:222 , PHE B:48 , PHE B:110 , TYR B:116 , PRO B:210 , PHE B:214 , ALA B:287 , PHE B:290 , ALA B:291 , MET B:460 , VAL B:461 , HEM B:1450 , HOH B:2011 , HOH B:2067 , HOH B:2252	BINDING SITE FOR RESIDUE T9H B1460

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

Asymmetric Unit

No.	Residues
1	Gly A:73	-	Gly A:74

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 4COH)

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:442
 aligned with CP51_TRYCC | Q7Z1V1 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:449
                                    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 TDPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKEEASKDNNTSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRKKK 478
               SCOP domains d4coha_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.hhhhhhhhhh.....eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.-------..hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......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
                 4coh A  30 TDPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKE-------TSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRKKK 478
                                    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         
                                                                                                                                                                                                                                                      250     258

Chain B from PDB  Type:PROTEIN  Length:445
 aligned with CP51_TRYCC | Q7Z1V1 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:452
                                    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 PTDPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKEEASKDNNTSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRKKKLP 480
               SCOP domains d4cohb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.hhhhhhhhhh.....eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.-------..hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......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
                 4coh B  29 PTDPPVYPVTVPFLGHIVQFGKNPLEFMQRCKRDLKSGVFTISIGGQRVTIVGDPHEHSRFFSPRNEILSPREVYTIMTPVFGEGVAYAAPYPRMREQLNFLAEELTIAKFQNFVPAIQHEVRKFMAENWKEDEGVINLLEDCGAMIINTACQCLFGEDLRKRLNARHFAQLLSKMESSLIPAAVFMPWLLRLPLPQSARCREARAELQKILGEIIVAREKE-------TSDLLGGLLKAVYRDGTRMSLHEVCGMIVAAMFAGQHTSTITTSWSMLHLMHPKNKKWLDKLHKEIDEFPAQLNYDNVMDEMPFAERCVRESIRRDPPLLMVMRMVKAEVKVGSYVVPKGDIIACSPLLSHHDEEAFPNPRLWDPERDEKVDGAFIGFGAGVHKCIGQKFALLQVKTILATAFREYDFQLLRDEVPDPDYHTMVVGPTLNQCLVKYTRKKKLP 480
                                    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  
                                                                                                                                                                                                                                                       250     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(

)

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	d4coha_	A:
1b	d4cohb_	B:

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

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

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:73 - Gly A:74	[ RasMol ]

Biological Units
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	4coh
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	CP51_TRYCC \| Q7Z1V1
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(no "Related Entries Specified in the PDB File" available for 4COH)

Description

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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)

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Exons (0, 0)

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