2BDM - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF CYTOCHROME P450 2B4 WITH BOUND BIFONAZOLE

Authors :   Y. Zhao, M. A. White, B. K. Muralidhara, L. Sun, J. R. Halpert, C. D. Stout

Date :   20 Oct 05 (Deposition) - 27 Dec 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: A  (2x)

Keywords :   P450, Monooxygenase, Oxidoreductase, Membrane Protein, Cyp 2B4, Cyp Lm2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhao, M. A. White, B. K. Muralidhara, L. Sun, J. R. Halpert, C. D. Stou
Structure Of Microsomal Cytochrome P450 2B4 Complexed With The Antifungal Drug Bifonazole: Insight Into P450 Conformational Plasticity And Membrane Interaction.
J. Biol. Chem. V. 281 5973 2006
PubMed-ID: 16373351 | Reference-DOI: 10.1074/JBC.M511464200
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME P450 2B4
	Chains	:	A
	EC Number	:	1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK
	Expression System Strain	:	TOPP3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 28-491
	Gene	:	CYP2B4
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	CYPIIB4, P450-LM2, ISOZYME 2, P450 TYPES B0 AND B1

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CM5	4	Ligand/Ion	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	TMI	3	Ligand/Ion	1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	CM5	4	Ligand/Ion	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	TMI	3	Ligand/Ion	1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE

Biological Unit 2 (3, 16)

No.	Name	Count	Type	Full Name
1	CM5	8	Ligand/Ion	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	TMI	6	Ligand/Ion	1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE

Biological Unit 3 (3, 16)

No.	Name	Count	Type	Full Name
1	CM5	8	Ligand/Ion	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	TMI	6	Ligand/Ion	1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:220 , THR A:302 , THR A:306 , VAL A:367 , HIS A:369 , LEU A:392 , PRO A:428 , PHE A:429 , SER A:430 , ARG A:434 , CYS A:436 , TMI A:501 , CM5 A:504 , HOH A:610 , HOH A:632 , HOH A:670	BINDING SITE FOR RESIDUE HEM A 500
2	AC2	SOFTWARE	SER A:128 , MET A:132 , SER A:213 , PHE A:217 , PHE A:220 , LEU A:295 , PHE A:296 , ALA A:298 , GLY A:299 , THR A:302 , ILE A:363 , HEM A:500 , CM5 A:504	BINDING SITE FOR RESIDUE TMI A 501
3	AC3	SOFTWARE	PRO A:106 , PHE A:184 , LEU A:198 , PHE A:202 , ASN A:287 , LEU A:290 , THR A:291 , LEU A:293 , SER A:294 , PHE A:297	BINDING SITE FOR RESIDUE TMI A 502
4	AC4	SOFTWARE	GLN A:45 , MET A:46 , ARG A:48 , LEU A:51 , VAL A:68 , TYR A:69 , LEU A:70 , VAL A:104 , GLU A:218 , PHE A:223 , PHE A:365 , VAL A:477 , CM5 A:507	BINDING SITE FOR RESIDUE TMI A 503
5	AC5	SOFTWARE	GLU A:93 , PHE A:108 , ARG A:125 , LEU A:129 , LEU A:219 , LYS A:433 , HEM A:500 , TMI A:501 , HOH A:610 , HOH A:663 , HOH A:678	BINDING SITE FOR RESIDUE CM5 A 504
6	AC6	SOFTWARE	ARG A:98 , ILE A:101 , ILE A:114 , PHE A:115 , GLY A:118 , ARG A:122 , TYR A:226	BINDING SITE FOR RESIDUE CM5 A 505
7	AC7	SOFTWARE	LEU A:40 , VAL A:249 , GLU A:250 , ARG A:253 , PHE A:264 , TYR A:268 , GLN A:286 , LEU A:293	BINDING SITE FOR RESIDUE CM5 A 506
8	AC8	SOFTWARE	PRO A:34 , SER A:35 , LEU A:37 , LEU A:51 , SER A:54 , ARG A:57 , PHE A:365 , TMI A:503	BINDING SITE FOR RESIDUE CM5 A 507

(no "SS Bond" information available for 2BDM)

Asymmetric Unit

No.	Residues
1	Leu A:37	-	Pro A:38

Asymmetric Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CP2B4_RABIT_001 *	V	39	I	CP2B4_RABIT	---	---	A	V	39	I
2	UniProt	VAR_CP2B4_RABIT_002 *	I	174	V	CP2B4_RABIT	---	---	A	I	174	V
3	UniProt	VAR_CP2B4_RABIT_003 *	L	290	I	CP2B4_RABIT	---	---	A	L	290	I
4	UniProt	VAR_CP2B4_RABIT_004 *	M	314	L	CP2B4_RABIT	---	---	A	M	314	L
5	UniProt	VAR_CP2B4_RABIT_005 *	L	420	M	CP2B4_RABIT	---	---	A	L	420	M
	* ID not provided by source

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

Biological Unit 1 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CP2B4_RABIT_001 *	V	39	I	CP2B4_RABIT	---	---	A	V	39	I
2	UniProt	VAR_CP2B4_RABIT_002 *	I	174	V	CP2B4_RABIT	---	---	A	I	174	V
3	UniProt	VAR_CP2B4_RABIT_003 *	L	290	I	CP2B4_RABIT	---	---	A	L	290	I
4	UniProt	VAR_CP2B4_RABIT_004 *	M	314	L	CP2B4_RABIT	---	---	A	M	314	L
5	UniProt	VAR_CP2B4_RABIT_005 *	L	420	M	CP2B4_RABIT	---	---	A	L	420	M
	* ID not provided by source

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

Biological Unit 2 (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CP2B4_RABIT_001 *	V	39	I	CP2B4_RABIT	---	---	A	V	39	I
2	UniProt	VAR_CP2B4_RABIT_002 *	I	174	V	CP2B4_RABIT	---	---	A	I	174	V
3	UniProt	VAR_CP2B4_RABIT_003 *	L	290	I	CP2B4_RABIT	---	---	A	L	290	I
4	UniProt	VAR_CP2B4_RABIT_004 *	M	314	L	CP2B4_RABIT	---	---	A	M	314	L
5	UniProt	VAR_CP2B4_RABIT_005 *	L	420	M	CP2B4_RABIT	---	---	A	L	420	M
	* ID not provided by source

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

Biological Unit 3 (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CP2B4_RABIT_001 *	V	39	I	CP2B4_RABIT	---	---	A	V	39	I
2	UniProt	VAR_CP2B4_RABIT_002 *	I	174	V	CP2B4_RABIT	---	---	A	I	174	V
3	UniProt	VAR_CP2B4_RABIT_003 *	L	290	I	CP2B4_RABIT	---	---	A	L	290	I
4	UniProt	VAR_CP2B4_RABIT_004 *	M	314	L	CP2B4_RABIT	---	---	A	M	314	L
5	UniProt	VAR_CP2B4_RABIT_005 *	L	420	M	CP2B4_RABIT	---	---	A	L	420	M
	* ID not provided by source

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP2B4_RABIT	429-438	1	A:429-438

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.	CP2B4_RABIT	429-438	1	A:429-438

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP2B4_RABIT	429-438	2	A:429-438

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP2B4_RABIT	429-438	2	A:429-438

(no "Exon" information available for 2BDM)

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
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Chain A from PDB  Type:PROTEIN  Length:465
 aligned with CP2B4_RABIT | P00178 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   | 
          CP2B4_RABIT    28 GRLPPGPSPLPVLGNLLQMDRKGLLRSFLRLREKYGDVFTVYLGSRPVVVLCGTDAIREALVDQAEAFSGRGKIAVVDPIFQGYGVIFANGERWRALRRFSLATMRDFGMGKRSVEERIQEEARCLVEELRKSKGALLDNTLLFHSITSNIICSIVFGKRFDYKDPVFLRLLDLFFQSFSLISSFSSQVFELFPGFLKHFPGTHRQIYRNLQEINTFIGQSVEKHRATLDPSNPRDFIDVYLLRMEKDKSDPSSEFHHQNLILTVLSLFFAGTETTSTTLRYGFLLMLKYPHVTERVQKEIEQVIGSHRPPALDDRAKMPYTDAVIHEIQRLGDLIPFGVPHTVTKDTQFRGYVIPKNTEVFPVLSSALHDPRYFETPNTFNPGHFLDANGALKRNEGFMPFSLGKRICLGEGIARTELFLFFTTILQNFSIASPVPPEDIDLTPRESGVGNVPPSYQIRFLAR-   -
               SCOP domains d2bdma_ A: Mammalian cytochrome p450 2b4                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2bdmA00 A:28-492 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhh.eeeeee..eeeeeehhhhhhhhhhh.......ee..................hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeee...hhhhh..................eeee.. Sec.struct. author
                 SAPs(SNPs) -----------I--------------------------------------------------------------------------------------------------------------------------------------V-------------------------------------------------------------------------------------------------------------------I-----------------------L---------------------------------------------------------------------------------------------------------M------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bdm A  28 GKLPPGPSPLPVLGNLLQMDRKGLLRSFLRLREKYGDVFTVYLGSRPVVVLCGTDAIREALVDQAEAFSGRGKIAVVDPIFQGYGVIFANGERWRALRRFSLATMRDFGMGKRSVEERIQEEARCLVEELRKSKGALLDNTLLFHSITSNIICSIVFGKRFDYKDPVFLRLLDLFFQSFSLISSFSSQVFELFSGFLKYFPGTHRQIYRNLQEINTFIGQSVEKHRATLDPSNPRDFIDVYLLRMEKDKSDPSSEFHHQNLILTVLSLFFAGTETTSTTLRYGFLLMLKYPHVTERVQKEIEQVIGSHRPPALDDRAKMPYTDAVIHEIQRLGDLIPFGVPHTVTKDTQFRGYVIPKNTEVFPVLSSALHDPRYFETPNTFNPGHFLDANGALKRNEGFMPFSLGKRICLGEGIARTELFLFFTTILQNFSIASPVPPEDIDLTPRESGVGNVPPSYQIRFLARH 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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome P450 (480)

Superfamily: Cytochrome P450 (480)

Family: Cytochrome P450 (323)

Protein domain: Mammalian cytochrome p450 2b4 (10)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (10)

d2bdma_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome p450 (271)

Homologous Superfamily: Cytochrome p450 (271)

Rabbit (Oryctolagus cuniculus) (7)

2bdmA00

A:28-492

(no "Pfam Domain" information available for 2BDM)

Asymmetric Unit(hide GO term definitions)

Chain A (CP2B4_RABIT | P00178)

molecular function
	GO:0070330	aromatase activity	Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
	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.
biological process
	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.
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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	Cis Peptide Bonds
		Leu A:37 - Pro A:38	[ RasMol ]

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	2bdm
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1po5	CRYSTAL STRUCTURE OF MAMMALIAN CYTOCHROME P450 2B4
1suo	CRYSTAL STRUCTURE OF MAMMALIAN CYTOCHROME P450 2B4 WITH BOUND 4-(4-CHLOROPHENYL)IMIDAZOLE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

PROSITE Motifs (1, 1)

Exons (0, 0)

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