3IBD - JenaLib

Title :   CRYSTAL STRUCTURE OF A CYTOCHROME P450 2B6 GENETIC VARIANT IN COMPLEX WITH THE INHIBITOR 4-(4-CHLOROPHENYL)IMIDAZOLE

Authors :   S. C. Gay, L. Sun, J. C. Talakad, M. B. Shah, D. C. Stout, J. R. Halpert

Date :   15 Jul 09 (Deposition) - 19 Jan 10 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   P450, Cytochrome P450 2B6, Monooxygenase, Oxidoreductase, Membrane Protein, Cyp 2B6, Endoplasmic Reticulum, Heme, Iron, Membrane, Metal-Binding, Microsome, Phosphoprotein, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Gay, M. B. Shah, J. C. Talakad, K. Maekawa, A. G. Roberts, P. R. Wilderman, L. Sun, J. Y. Yang, S. C. Huelga, W. X. Hong, Q. Zhang, C. D. Stout, J. R. Halpert
Crystal Structure Of A Cytochrome P450 2B6 Genetic Variant In Complex With The Inhibitor 4-(4-Chlorophenyl)Imidazole A 2. 0-A Resolution.
Mol. Pharmacol. V. 77 529 2010
PubMed-ID: 20061448 | Reference-DOI: 10.1124/MOL.109.062570

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:14 , ARG A:98 , VAL A:113 , ILE A:114 , TRP A:121 , ARG A:125 , ALA A:298 , GLY A:299 , THR A:302 , THR A:303 , THR A:306 , GLN A:357 , LEU A:363 , VAL A:367 , HIS A:369 , LEU A:392 , PRO A:428 , PHE A:429 , SER A:430 , ARG A:434 , CYS A:436 , LEU A:437 , GLY A:438 , CPZ A:501	BINDING SITE FOR RESIDUE HEM A 500
2	AC2	SOFTWARE	PHE A:297 , ALA A:298 , THR A:302 , VAL A:367 , HOH A:497 , HEM A:500	BINDING SITE FOR RESIDUE CPZ A 501
3	AC3	SOFTWARE	PHE A:188 , GLU A:194 , MET A:198 , PHE A:202 , TYR A:244 , PHE A:296	BINDING SITE FOR RESIDUE CM5 A 1001
4	AC4	SOFTWARE	ASP A:47 , LEU A:51	BINDING SITE FOR RESIDUE CM5 A 1002
5	AC5	SOFTWARE	LYS A:91 , ALA A:92 , GLU A:93 , ALA A:94 , SER A:461 , PRO A:462	BINDING SITE FOR RESIDUE SCN A 1003
6	AC6	SOFTWARE	ALA A:321 , GLU A:322 , MET A:459 , ARG A:491 , HOH A:607	BINDING SITE FOR RESIDUE SCN A 1004
7	AC7	SOFTWARE	TYR A:317 , PRO A:318 , HIS A:319	BINDING SITE FOR RESIDUE SCN A 1005
8	AC8	SOFTWARE	ARG A:57 , PHE A:58 , LYS A:61	BINDING SITE FOR RESIDUE SCN A 1006

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (16, 16)

Asymmetric/Biological Unit (16, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_025207	D	28	G	CP2B6_HUMAN	Polymorphism	33980385	A	G	28	G
02	UniProt	VAR_033819	R	29	P	CP2B6_HUMAN	Polymorphism	34284776	A	K	29	P
03	UniProt	VAR_025208	R	29	S	CP2B6_HUMAN	Polymorphism	33926104	A	K	29	S
04	UniProt	VAR_023564	M	46	V	CP2B6_HUMAN	Polymorphism	35303484	A	M	46	V
05	UniProt	VAR_023565	G	99	E	CP2B6_HUMAN	Polymorphism	36060847	A	G	99	E
06	UniProt	VAR_016948	K	139	E	CP2B6_HUMAN	Polymorphism	12721655	A	K	139	E
07	UniProt	VAR_023566	R	140	Q	CP2B6_HUMAN	Polymorphism	35773040	A	R	140	Q
08	UniProt	VAR_016924	P	167	A	CP2B6_HUMAN	Polymorphism	3826711	A	P	167	A
09	UniProt	VAR_016925	Q	172	H	CP2B6_HUMAN	Polymorphism	3745274	A	Q	172	H
10	UniProt	VAR_016928	S	259	R	CP2B6_HUMAN	Polymorphism	45482602	A	S	259	R
11	UniProt	VAR_016926	K	262	R	CP2B6_HUMAN	Polymorphism	2279343	A	R	262	R
12	UniProt	VAR_025209	N	289	K	CP2B6_HUMAN	Polymorphism	34277950	A	N	289	K
13	UniProt	VAR_025210	T	306	S	CP2B6_HUMAN	Polymorphism	34698757	A	T	306	S
14	UniProt	VAR_024716	I	328	T	CP2B6_HUMAN	Polymorphism	28399499	A	I	328	T
15	UniProt	VAR_023567	I	391	N	CP2B6_HUMAN	Polymorphism	35979566	A	I	391	N
16	UniProt	VAR_016929	R	487	C	CP2B6_HUMAN	Polymorphism	3211371	A	R	487	C

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

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:465
 aligned with CP2B6_HUMAN | P20813 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         491 
                                    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       487   | 
          CP2B6_HUMAN    28 DRLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFGMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKYFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPKDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPR-   -
               SCOP domains d3ibda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3ibdA00 A:28-492 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...hhhhee.....hhhhhh.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee......eeee.. Sec.struct. author
             SAPs(SNPs) (1) GP----------------V----------------------------------------------------E---------------------------------------EQ--------------------------A----H--------------------------------------------------------------------------------------R--R--------------------------K----------------S---------------------T--------------------------------------------------------------N-----------------------------------------------------------------------------------------------C----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ibd A  28 GKLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFGMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPRH 492
                                    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       487

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CP2B6_HUMAN | P20813)

molecular function
	GO:0008392	arachidonic acid epoxygenase activity	Catalysis of an NADPH- and oxygen-dependent reaction that converts arachidonic acid to a cis-epoxyeicosatrienoic acid.
	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:0016712	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0008395	steroid hydroxylase activity	Catalysis of the formation of a hydroxyl group on a steroid by incorporation of oxygen from O2.
biological process
	GO:0042180	cellular ketone metabolic process	The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
	GO:0017144	drug metabolic process	The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
	GO:0019373	epoxygenase P450 pathway	The chemical reactions and pathways by which arachidonic acid is converted to other compounds including epoxyeicosatrienoic acids and dihydroxyeicosatrienoic acids.
	GO:0042738	exogenous drug catabolic process	The chemical reactions and pathways resulting in the breakdown of a drug that has originated externally to the cell or organism.
	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:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	GO:0006805	xenobiotic metabolic process	The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031090	organelle membrane	A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

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