4RQL - 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)

Title :   CRYSTAL STRUCTURE OF A HUMAN CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH A MONOTERPENE - SABINENE

Authors :   M. B. Shah

Date :   03 Nov 14 (Deposition) - 28 Jan 15 (Release) - 11 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   P450, Cytochrome P450 2B6, Monooxygenase, Membrane Protein, Cyp2B6, Endoplasmic Reticulum, Heme, Iron, Metal Binding, Microsome, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. B. Shah, P. R. Wilderman, J. Liu, H. H. Jang, Q. Zhang, C. D. Stout, J. R. Halpert
Structural And Biophysical Characterization Of Human Cytochromes P450 2B6 And 2A6 Bound To Volatile Hydrocarbons Analysis And Comparison.
Mol. Pharmacol. V. 87 649 2015
PubMed-ID: 25585967 | Reference-DOI: 10.1124/MOL.114.097014

Molecule 1 - CYTOCHROME P450 2B6
	Chains	:	A, B
	EC Number	:	1.14.13.-, 1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CYP2B6
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	1,4-CINEOLE 2-EXO-MONOOXYGENASE, CYPIIB6, CYTOCHROME P450 IIB1

		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, 12)

No.	Name	Count	Type	Full Name
1	CM5	6	Ligand/Ion	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	SNE	2	Ligand/Ion	SABINENE

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	CM5	3	Ligand/Ion	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	SNE	1	Ligand/Ion	SABINENE

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	CM5	3	Ligand/Ion	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	SNE	1	Ligand/Ion	SABINENE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:98 , VAL A:113 , ILE A:114 , TRP A:121 , ARG A:125 , ALA A:298 , THR A:302 , THR A:306 , GLN A:357 , LEU A:362 , 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 , ALA A:442 , HOH A:688	BINDING SITE FOR RESIDUE HEM A 501
02	AC2	SOFTWARE	PHE A:220 , PHE A:223	BINDING SITE FOR RESIDUE CM5 A 502
03	AC3	SOFTWARE	GLU A:194 , PHE A:195 , TYR A:244 , PHE A:296 , HOH A:745	BINDING SITE FOR RESIDUE CM5 A 503
04	AC4	SOFTWARE	MET A:46 , ARG A:48	BINDING SITE FOR RESIDUE CM5 A 504
05	AC5	SOFTWARE	PHE A:297 , ALA A:298 , THR A:302	BINDING SITE FOR RESIDUE SNE A 505
06	AC6	SOFTWARE	GLU A:218 , MET A:365 , PRO A:368 , VAL A:477	BINDING SITE FOR RESIDUE EDO A 506
07	AC7	SOFTWARE	ARG B:98 , VAL B:113 , ILE B:114 , TRP B:121 , ARG B:125 , MET B:132 , ILE B:179 , ALA B:298 , GLY B:299 , THR B:302 , THR B:306 , GLN B:357 , LEU B:362 , LEU B:363 , HIS B:369 , LEU B:392 , PRO B:428 , PHE B:429 , SER B:430 , ARG B:434 , CYS B:436 , LEU B:437 , GLY B:438 , ALA B:442 , HOH B:745	BINDING SITE FOR RESIDUE HEM B 501
08	AC8	SOFTWARE	PHE B:297 , THR B:302	BINDING SITE FOR RESIDUE SNE B 502
09	AC9	SOFTWARE	GLU B:194 , MET B:198 , PHE B:202 , TYR B:244 , HIS B:247 , PHE B:296	BINDING SITE FOR RESIDUE CM5 B 503
10	BC1	SOFTWARE	MET B:46 , ARG B:48 , GLY B:50	BINDING SITE FOR RESIDUE CM5 B 504
11	BC2	SOFTWARE	PHE B:223	BINDING SITE FOR RESIDUE CM5 B 505
12	BC3	SOFTWARE	GLU B:218 , MET B:365 , PRO B:368 , HOH B:778	BINDING SITE FOR RESIDUE EDO B 506

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

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

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

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

(no "Exon" information available for 4RQL)

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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.hhhhhhee.....hhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee......eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rql 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

Chain B from PDB  Type:PROTEIN  Length:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeeehhhhhhhhhhh.hhhhhhee.....hhhhhh.......hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee......eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rql B  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 '\|'

(no "SCOP Domain" information available for 4RQL)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CM5	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SNE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

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

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4rql
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CP2B6_HUMAN \| P20813
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.14.13.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	1.14.14.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CP2B6_HUMAN \| P20813
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CP2B6_HUMAN \| P20813	:	3ibd 3qoa 3qu8 3ua5 4i91 4rrt 4zv8 5uap 5uda 5uec 5ufg

3ibd	CRYSTAL STRUCTURE OF A CYTOCHROME P450 2B6 GENETIC VARIANT IN COMPLEX WITH THE INHIBITOR 4-(4-CHLOROPHENYL)IMIDAZOLE
3qoa	CRYSTAL STRUCTURE OF A HUMAN CYTOCHROME P450 2B6 (Y226H/ K262R) IN COMPLEX WITH THE INHIBITOR 4-BENZYLPYRIDINE
3qu8	CRYSTAL STRUCTURE OF A HUMAN CYTOCHROME P450 2B6 (Y226H/ K262R) IN COMPLEX WITH THE INHIBITOR 4-(4-NITROBENZYL) PYRIDINE
3ua5	CRYSTAL STRUCTURE OF CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH TWO MOLECULES OF AMLODIPINE
4i91	CRYSTAL STRUCTURE OF CYTOCHROME P450 2B6 (Y226H/K262R) IN COMPLEX WITH ALPHA-PINENE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (22, 22)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File