4WNW - JenaLib

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Title :   HUMAN CYTOCHROME P450 2D6 THIORIDAZINE COMPLEX

Authors :   A. Wang, C. D. Stout, E. F. Johnson

Date :   14 Oct 14 (Deposition) - 14 Jan 15 (Release) - 04 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Cyp2D6, P450 2D6, P450, Monooxygenase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Wang, C. D. Stout, Q. Zhang, E. F. Johnson
Contributions Of Ionic Interactions And Protein Dynamics To Cytochrome P450 2D6 (Cyp2D6) Substrate And Inhibitor Binding.
J. Biol. Chem. V. 290 5092 2015
PubMed-ID: 25555909 | Reference-DOI: 10.1074/JBC.M114.627661

Molecule 1 - CYTOCHROME P450 2D6
	Chains	:	A, B
	EC Number	:	1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCWORI
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 34-497
	Gene	:	CYP2D6, CYP2DL1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYPIID6,CYTOCHROME P450-DB1,DEBRISOQUINE 4-HYDROXYLASE

		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 (4, 7)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NA	2	Ligand/Ion	SODIUM ION
3	NI	1	Ligand/Ion	NICKEL (II) ION
4	RTZ	2	Ligand/Ion	10-{2-[(2R)-1-METHYLPIPERIDIN-2-YL]ETHYL}-2-(METHYLSULFANYL)-10H-PHENOTHIAZINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NA	-1	Ligand/Ion	SODIUM ION
3	NI	-1	Ligand/Ion	NICKEL (II) ION
4	RTZ	1	Ligand/Ion	10-{2-[(2R)-1-METHYLPIPERIDIN-2-YL]ETHYL}-2-(METHYLSULFANYL)-10H-PHENOTHIAZINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	NA	-1	Ligand/Ion	SODIUM ION
3	NI	-1	Ligand/Ion	NICKEL (II) ION
4	RTZ	1	Ligand/Ion	10-{2-[(2R)-1-METHYLPIPERIDIN-2-YL]ETHYL}-2-(METHYLSULFANYL)-10H-PHENOTHIAZINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:101 , VAL A:119 , PHE A:120 , TRP A:128 , ARG A:132 , ILE A:186 , ALA A:305 , GLY A:306 , THR A:309 , THR A:313 , VAL A:374 , HIS A:376 , LEU A:399 , PRO A:435 , PHE A:436 , SER A:437 , ARG A:441 , CYS A:443 , GLY A:445 , LEU A:448	binding site for residue HEM A 601
2	AC2	SOFTWARE	PHE A:112 , PHE A:120 , ALA A:209 , GLY A:212 , LEU A:213 , GLU A:216 , GLN A:244 , PHE A:247 , ASP A:301 , SER A:304 , ALA A:305 , VAL A:308 , VAL A:374 , PHE A:483	binding site for residue RTZ A 602
3	AC3	SOFTWARE	GLU A:216	binding site for residue NA A 603
4	AC4	SOFTWARE	ARG B:101 , VAL B:119 , PHE B:120 , TRP B:128 , ARG B:132 , LEU B:302 , ALA B:305 , GLY B:306 , THR B:309 , THR B:313 , VAL B:374 , HIS B:376 , LEU B:399 , PRO B:435 , PHE B:436 , SER B:437 , ARG B:441 , CYS B:443 , GLY B:445	binding site for residue HEM B 601
5	AC5	SOFTWARE	PHE B:112 , PHE B:120 , LEU B:121 , ALA B:209 , GLY B:212 , LEU B:213 , GLU B:216 , GLN B:244 , ALA B:300 , ASP B:301 , SER B:304 , ALA B:305 , VAL B:308 , PHE B:483	binding site for residue RTZ B 602
6	AC6	SOFTWARE	GLU B:216 , ARG B:221	binding site for residue NA B 603
7	AC7	SOFTWARE	HIS B:258 , ASP B:270 , GLU B:273 , GLU B:287	binding site for residue NI B 604

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

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

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

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

(no "Exon" information available for 4WNW)

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:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhh....eeeeee..eeeeee.hhhhhhhhhh.hhhhh.....hhhhhh...............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhhheee...........eee...eee.....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wnw A  33 LPPGPLPLPGLGNLLHVDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREALVTHGEDTADRPPVPITQILGFGPRSQGVFLARYGPAWREQRRFSVSTLRNLKSLEQWVTEEAACLCAAFANHSGRPFRPNGLLDKAVSNVIASLTCGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVLLHIPALAGKVLRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAEMEKAKGNPESSFNDENLRIVVADLFSAGMVTTSTTLAWGLLLMILHPDVQRRVQQEIDDVIGQVRRPEMGDQAHMPYTTAVIHEVQRFGDIVPLGVTHMTSRDIEVQGFRIPKGTTLITNLSSVLKDEAVWEKPFRFHPEHFLDAQGHFVKPEAFLPFSAGRRACLGEPLARMELFLFFTSLLQHFSFSVPTGQPRPSHHGVFAFLVSPSPYELCAVPR 497
                                    42        52        62        72        82        92       102       112       122       132       142|      156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496 
                                                                                                                                       142|                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                        147

Chain B from PDB  Type:PROTEIN  Length:452
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh....hhhhhhhhhhhhhh...eee....eeeeehhhhhhhhhhh.hhhhhh....hhhhhh...............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhh.eee...........eee...eee.....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wnw B  33 LPPGPLPLPGLGNLLHVDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREALVTHGEDTADRPPVPITQILGFGPRSQGVFLARYGPAWREQRRFSVSTLRNLSLEQWVTEEAACLCAAFANHSGRPFRPNGLLDKAVSNVIASLTCGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVGKVLRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAEMEKAKGNPESSFNDENLRIVVADLFSAGMVTTSTTLAWGLLLMILHPDVQRRVQQEIDDVIGQVRRPEMGDQAHMPYTTAVIHEVQRFGDIVPLGVTHMTSRDIEVQGFRIPKGTTLITNLSSVLKDEAVWEKPFRFHPEHFLDAQGHFVKPEAFLPFSAGRRACLGEPLARMELFLFFTSLLQHFSFSVPTGQPRPSHHGVFAFLVSPSPYELCAVPR 497
                                    42        52        62        72        82        92       102       112       122       132       142|      157       167       177       187       197       207       217       227 ||    245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495  
                                                                                                                                       142|                                                                              229|                                                                                                                                                                                                                                                                   
                                                                                                                                        148                                                                               238

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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 4WNW)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4wnw)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4wnw
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		Orientation in Membranes	:	OPM
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	CP2D6_HUMAN \| P10635
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	1.14.14.1
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UniProtKB/Swiss-Prot
	CP2D6_HUMAN \| P10635	:	2f9q 3qm4 3tbg 3tda 4wnt 4wnu 4wnv 4xry 4xrz 5tft 5tfu

2f9q	2F9Q CONTAINS THE V374V VARIANT OF THE PROTEIN CRYSTALLIZED IN AN OPEN FORM
3qm4	3QM4 CONTAINS THE SAME PROTEIN COMPLEXED WITH PRINOMASTAT
3tbg	3TBG CONTAINS THE SAME PROTEIN IN OPEN CONFORMATION COMPLEXED WITH 2 MOLECULES OF THIORIDAZINE
3tda	3TDA CONTAINS THE SAME PROTEIN COMPLEXED WITH PRINOMASTAT
4wnt
4wnu
4wnv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (34, 34)

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