3LXH - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CYTOCHROME P450 CYP101D1

Authors :   W. Yang, S. G. Bell, H. Wang, M. Bartlam, L. L. Wong, Z. Rao

Date :   25 Feb 10 (Deposition) - 23 Jun 10 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Cytochrome P450 Fold, Heme, Iron, Metal-Binding, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Yang, S. G. Bell, H. Wang, W. Zhou, N. Hoskins, A. Dale, M. Bartlam, L. L. Wong, Z. Rao
Molecular Characterization Of A Class I P450 Electron Transfer System From Novosphingobium Aromaticivorans Dsm12444
J. Biol. Chem. V. 285 27372 2010
PubMed-ID: 20576606 | Reference-DOI: 10.1074/JBC.M110.118349

Molecule 1 - CYTOCHROME P450
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SARO_0514
	Organism Scientific	:	NOVOSPHINGOBIUM AROMATICIVORANS
	Organism Taxid	:	279238
	Strain	:	DSM 12444
	Synonym	:	CYTOCHROME P450 CYP101D1

		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 (3, 9)

No.	Name	Count	Type	Full Name
1	DIO	1	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PO4	6	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	DIO	1	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	DIO	-1	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:102 , THR A:103 , HIS A:110 , ARG A:114 , PHE A:165 , LEU A:252 , LEU A:253 , GLY A:256 , GLY A:257 , THR A:260 , ASP A:305 , ARG A:307 , THR A:357 , PRO A:362 , HIS A:363 , CYS A:365 , GLY A:367 , DIO A:423 , HOH A:463 , HOH A:492	BINDING SITE FOR RESIDUE HEM A 422
2	AC2	SOFTWARE	LEU A:252 , LEU A:255 , HEM A:422 , HOH A:463	BINDING SITE FOR RESIDUE DIO A 423
3	AC3	SOFTWARE	ARG A:13 , ARG A:26 , GLN A:49 , THR A:52 , HOH A:552 , HOH A:580	BINDING SITE FOR RESIDUE PO4 A 424
4	AC4	SOFTWARE	HIS A:316 , GLY A:317 , HOH A:682 , ARG B:78 , HOH B:484	BINDING SITE FOR RESIDUE PO4 A 425
5	AC5	SOFTWARE	ASP A:342 , PRO A:343 , MET A:344 , HOH A:452 , HOH A:455 , HOH A:459	BINDING SITE FOR RESIDUE PO4 A 426
6	AC6	SOFTWARE	ARG A:364 , ARG A:372	BINDING SITE FOR RESIDUE PO4 A 427
7	AC7	SOFTWARE	PRO B:102 , THR B:103 , HIS B:110 , ARG B:114 , PHE B:165 , LEU B:253 , GLY B:256 , GLY B:257 , THR B:260 , VAL B:261 , ASP B:305 , ARG B:307 , THR B:357 , PRO B:362 , HIS B:363 , CYS B:365 , GLY B:367 , HOH B:453 , HOH B:462	BINDING SITE FOR RESIDUE HEM B 422
8	AC8	SOFTWARE	ASP B:342 , PRO B:343 , MET B:344 , HOH B:447 , HOH B:454	BINDING SITE FOR RESIDUE PO4 B 423
9	AC9	SOFTWARE	ARG B:26 , GLN B:49 , THR B:52 , HOH B:477	BINDING SITE FOR RESIDUE PO4 B 424

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

Asymmetric Unit

No.	Residues
1	Val A:90	-	Pro A:91
2	Val A:101	-	Pro A:102
3	Pro A:107	-	Pro A:108
4	Gly A:222	-	Ser A:223
5	Ser A:223	-	Gly A:224
6	Val B:90	-	Pro B:91
7	Val B:101	-	Pro B:102
8	Pro B:107	-	Pro B:108
9	Gly B:222	-	Ser B:223
10	Ser B:223	-	Gly B:224

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

(no "PROSITE Motif" information available for 3LXH)

(no "Exon" information available for 3LXH)

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:408
 aligned with Q2GB12_NOVAD | Q2GB12 from UniProtKB/TrEMBL  Length:421

    Alignment length:408
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409        
         Q2GB12_NOVAD    10 QKHRVAPPPHVPGHLIREIDAYDLDGLEQGFHEAWKRVQQPDTPPLVWTPFTGGHWIATRGTLIDEIYRSPERFSSRVIWVPREAGEAYDMVPTKLDPPEHTPYRKAIDKGLNLAEIRKLEDQIRTIAVEIIEGFADRGHCEFGSEFSTVFPVRVFLALAGLPVEDATKLGLLANEMTRPSGNTPEEQGRSLEAANKGFFEYVAPIIAARRGGSGTDLITRILNVEIDGKPMPDDRALGLVSLLLLGGLDTVVNFLGFMMIYLSRHPETVAEMRREPLKLQRGVEELFRRFAVVSDARYVVSDMEFHGTMLKEGDLILLPTALHGLDDRHHDDPMTVDLSRRDVTHSTFAQGPHRCAGMHLARLEVTVMLQEWLARIPEFRLKDRAVPIYHSGIVAAVENIPLEWEPQ 417
               SCOP domains d3lxha_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhh.........hhhhhhhhhhhhhh......eeee.....eeee.hhhhhhhhhh....ee......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhhh........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee......eee.....eee..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lxh A  10 QKHRVAPPPHVPGHLIREIDAYDLDGLEQGFHEAWKRVQQPDTPPLVWTPFTGGHWIATRGTLIDEIYRSPERFSSRVIWVPREAGEAYDMVPTKLDPPEHTPYRKAIDKGLNLAEIRKLEDQIRTIAVEIIEGFADRGHCEFGSEFSTVFPVRVFLALAGLPVEDATKLGLLANEMTRPSGNTPEEQGRSLEAANKGFFEYVAPIIAARRGGSGTDLITRILNVEIDGKPMPDDRALGLVSLLLLGGLDTVVNFLGFMMIYLSRHPETVAEMRREPLKLQRGVEELFRRFAVVSDARYVVSDMEFHGTMLKEGDLILLPTALHGLDDRHHDDPMTVDLSRRDVTHSTFAQGPHRCAGMHLARLEVTVMLQEWLARIPEFRLKDRAVPIYHSGIVAAVENIPLEWEPQ 417
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409

Chain B from PDB  Type:PROTEIN  Length:405
 aligned with Q2GB12_NOVAD | Q2GB12 from UniProtKB/TrEMBL  Length:421

    Alignment length:405
                                    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     
         Q2GB12_NOVAD    12 HRVAPPPHVPGHLIREIDAYDLDGLEQGFHEAWKRVQQPDTPPLVWTPFTGGHWIATRGTLIDEIYRSPERFSSRVIWVPREAGEAYDMVPTKLDPPEHTPYRKAIDKGLNLAEIRKLEDQIRTIAVEIIEGFADRGHCEFGSEFSTVFPVRVFLALAGLPVEDATKLGLLANEMTRPSGNTPEEQGRSLEAANKGFFEYVAPIIAARRGGSGTDLITRILNVEIDGKPMPDDRALGLVSLLLLGGLDTVVNFLGFMMIYLSRHPETVAEMRREPLKLQRGVEELFRRFAVVSDARYVVSDMEFHGTMLKEGDLILLPTALHGLDDRHHDDPMTVDLSRRDVTHSTFAQGPHRCAGMHLARLEVTVMLQEWLARIPEFRLKDRAVPIYHSGIVAAVENIPLEWEP 416
               SCOP domains d3lxhb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-3lxhB01 B:189-398                                                                                                                                                                                            ------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-3lxhB02 B:189-398                                                                                                                                                                                            ------------------ Pfam domains (2)
         Sec.struct. author .........hhhhh.........hhhhhhhhhhhhhh......eeee.....eeee.hhhhhhhhhh....ee......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeehhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhhh........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee......eee.....eee..eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxh B  12 HRVAPPPHVPGHLIREIDAYDLDGLEQGFHEAWKRVQQPDTPPLVWTPFTGGHWIATRGTLIDEIYRSPERFSSRVIWVPREAGEAYDMVPTKLDPPEHTPYRKAIDKGLNLAEIRKLEDQIRTIAVEIIEGFADRGHCEFGSEFSTVFPVRVFLALAGLPVEDATKLGLLANEMTRPSGNTPEEQGRSLEAANKGFFEYVAPIIAARRGGSGTDLITRILNVEIDGKPMPDDRALGLVSLLLLGGLDTVVNFLGFMMIYLSRHPETVAEMRREPLKLQRGVEELFRRFAVVSDARYVVSDMEFHGTMLKEGDLILLPTALHGLDDRHHDDPMTVDLSRRDVTHSTFAQGPHRCAGMHLARLEVTVMLQEWLARIPEFRLKDRAVPIYHSGIVAAVENIPLEWEP 416
                                    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

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome P450 (480)

Superfamily: Cytochrome P450 (480)

Family: automated matches (157)

Protein domain: automated matches (157)

Novosphingobium aromaticivorans [TaxId: 279238] (11)

1a	d3lxha_	A:
1b	d3lxhb_	B:

(no "CATH Domain" information available for 3LXH)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: p450] (161)

Family: p450 (161)

Novosphingobium aromaticivorans (strain DSM 12444) (5)

1a	p450-3lxhB01	B:189-398
1b	p450-3lxhB02	B:189-398

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q2GB12_NOVAD | Q2GB12)

molecular function
	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.
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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:222 - Ser A:223	[ RasMol ]
		Gly B:222 - Ser B:223	[ RasMol ]
		Pro A:107 - Pro A:108	[ RasMol ]
		Pro B:107 - Pro B:108	[ RasMol ]
		Ser A:223 - Gly A:224	[ RasMol ]
		Ser B:223 - Gly B:224	[ RasMol ]
		Val A:101 - Pro A:102	[ RasMol ]
		Val A:90 - Pro A:91	[ RasMol ]
		Val B:101 - Pro B:102	[ RasMol ]
		Val B:90 - Pro B:91	[ RasMol ]

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	3lxh
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UniProtKB/TrEMBL
	Q2GB12_NOVAD \| Q2GB12	:	3lxi 4c9k 4c9l 4c9m 4c9n 4c9o 4c9p

3lxd	ASSOCIATE FERREDOXIN REDUCTASE ARR FROM NOVOSPHINGOBIUM AROMATICIVORANS
3lxf	ASSOCIATE [2FE-2S] FERREDOXIN ARX FROM NOVOSPHINGOBIUM AROMATICIVORANS
3lxi	CRYSTAL STRUCTURE OF CAMPHOR-BOUND CYP101D1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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