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Title :   STRUCTURE OF N-(12-IMIDAZOLYL-DODECANOYL)-L-LEUCINE INHIBITOR BOUND TO THE HEME DOMAIN OF CYTOCHROME P450-BM3

Authors :   D. R. Tomchick

Date :   19 Nov 07 (Deposition) - 30 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Protein-Substrate Complex, Hemeprotein, Electron Transport, Fad, Flavoprotein, Fmn, Iron, Membrane, Metal-Binding, Monooxygenase, Multifunctional Enzyme, Nadp, Oxidoreductase, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. C. Haines, B. Chen, D. R. Tomchick, M. Bondlela, A. Hegde, M. Machius J. A. Peterson
Crystal Structure Of Inhibitor-Bound P450Bm-3 Reveals Open Conformation Of Substrate Access Channel.
Biochemistry V. 47 3662 2008
PubMed-ID: 18298086 | Reference-DOI: 10.1021/BI7023964
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME P450 102
	Chains	:	A, B
	EC Number	:	1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEX-1
	Expression System Strain	:	DH5(ALPHA)F'IQ
	Expression System Vector Type	:	PLASMID
	Gene	:	CYP102A1, CYP102
	Organism Scientific	:	BACILLUS MEGATERIUM

		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, 6)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	LEH	2	Ligand/Ion	N-[12-(1H-IMIDAZOL-1-YL)DODECANOYL]-L-LEUCINE
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	LEH	1	Ligand/Ion	N-[12-(1H-IMIDAZOL-1-YL)DODECANOYL]-L-LEUCINE
3	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	LEH	1	Ligand/Ion	N-[12-(1H-IMIDAZOL-1-YL)DODECANOYL]-L-LEUCINE
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:23 , HOH B:501 , HOH B:502 , HOH B:503 , HOH B:504 , HOH B:505	BINDING SITE FOR RESIDUE MG B 470
2	AC2	SOFTWARE	LYS A:69 , LEU A:86 , PHE A:87 , TRP A:96 , ILE A:153 , ALA A:264 , GLY A:265 , THR A:269 , LEU A:322 , THR A:327 , ALA A:328 , PHE A:331 , PRO A:392 , PHE A:393 , GLY A:394 , ARG A:398 , ALA A:399 , CYS A:400 , ILE A:401 , GLY A:402 , PHE A:405 , LEH A:500 , HOH A:501 , HOH A:502 , HOH A:504 , HOH A:510 , HOH A:511 , HOH A:613	BINDING SITE FOR RESIDUE HEM A 470
3	AC3	SOFTWARE	VAL A:26 , TYR A:51 , ALA A:74 , LEU A:75 , VAL A:78 , PHE A:87 , MET A:185 , ALA A:264 , GLU A:435 , THR A:436 , LEU A:437 , HEM A:470	BINDING SITE FOR RESIDUE LEH A 500
4	AC4	SOFTWARE	LYS B:69 , LEU B:86 , PHE B:87 , TRP B:96 , ILE B:153 , ALA B:264 , THR B:268 , THR B:269 , LEU B:322 , THR B:327 , ALA B:328 , PHE B:331 , PRO B:392 , PHE B:393 , GLY B:394 , ARG B:398 , ALA B:399 , CYS B:400 , ILE B:401 , GLY B:402 , PHE B:405 , ALA B:406 , LEH B:500 , HOH B:506 , HOH B:512 , HOH B:513 , HOH B:515 , HOH B:519 , HOH B:578	BINDING SITE FOR RESIDUE HEM B 471
5	AC5	SOFTWARE	VAL B:26 , LEU B:75 , VAL B:78 , PHE B:87 , ALA B:264 , GLU B:435 , THR B:436 , LEU B:437 , HEM B:471 , HOH B:731	BINDING SITE FOR RESIDUE LEH B 500
6	AC6	SOFTWARE	ILE B:366 , TRP B:367 , ARG B:375 , ARG B:378 , ALA B:384 , ILE B:385 , HOH B:558	BINDING SITE FOR RESIDUE MES B 490

(no "SS Bond" information available for 3BEN)

(no "Cis Peptide Bond" information available for 3BEN)

(no "SAP(SNP)/Variant" information available for 3BEN)

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.	CPXB_BACMB	394-403	2	A:393-402 B:393-402

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.	CPXB_BACMB	394-403	1	A:393-402 -

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.	CPXB_BACMB	394-403	1	- B:393-402

(no "Exon" information available for 3BEN)

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:454
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:454
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454    
           CPXB_BACMB     5 EMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGG 458
               SCOP domains d3bena_ A: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3benA00 A:4-457 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eee..hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhh.hhhhhh......hhhhhh..............hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ben A   4 EMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGG 457
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453

Chain B from PDB  Type:PROTEIN  Length:457
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:457
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       
           CPXB_BACMB     2 TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGG 458
               SCOP domains d3benb_ B: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3benB00 B:1-457 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eee..hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhh.hhhhhh......hhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ben B   1 TIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGG 457
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450

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(

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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: Cytochrome P450 bm-3 (60)

Bacillus megaterium [TaxId: 1404] (60)

1a	d3bena_	A:
1b	d3benb_	B:

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)

Bacillus megaterium. (2)

1a	3benA00	A:4-457
1b	3benB00	B:1-457

(no "Pfam Domain" information available for 3BEN)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CPXB_BACMB | P14779)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0003958	NADPH-hemoprotein reductase activity	Catalysis of the reaction: NADPH + H+ + n oxidized hemoprotein = NADP+ + n reduced hemoprotein.
	GO:0070330	aromatase activity	Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(no "Cis Peptide Bonds" information available for 3ben)

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1bu7	SAME PROTEIN, SUBSTRATE FREE FORM
1jpz	SAME PROTEIN COMPLEXED WITH THE SUBSTRATE N-PALMITOYLGLYCINE

Description

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Ligands, Modified Residues, Ions (4, 6)

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