4C9M - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF SUBSTRATE FREE, GLYCEROL BOUND WILD TYPE CYP101D1

Authors :   D. Batabyal, T. L Poulos

Date :   02 Oct 13 (Deposition) - 04 Dec 13 (Release) - 19 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Oxidoreductase, Mono-Oxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Batabyal, T. L. Poulos
Crystal Structures And Functional Characterization Of Wild Type And Active Sites Mutants Of Cyp101D1.
Biochemistry V. 52 8898 2013
PubMed-ID: 24261604 | Reference-DOI: 10.1021/BI401330C

Molecule 1 - CYTOCHROME P450
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	NOVOSPHINGOBIUM AROMATICIVORANS
	Organism Taxid	:	48935
	Strain	:	DSM12444
	Synonym	:	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 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	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 , ASP B:305 , ARG B:307 , THR B:357 , PRO B:362 , HIS B:363 , CYS B:365 , GLY B:367 , GOL B:1419 , HOH B:2134 , HOH B:2307	BINDING SITE FOR RESIDUE HEM B1418
2	AC2	SOFTWARE	PRO A:102 , THR A:103 , HIS A:110 , ARG A:114 , PHE A:165 , LEU A:253 , GLY A:256 , GLY A:257 , THR A:260 , PHE A:264 , ASP A:305 , ARG A:307 , THR A:357 , ALA A:359 , PRO A:362 , HIS A:363 , CYS A:365 , GLY A:367 , GOL A:1419 , HOH A:2171 , HOH A:2383	BINDING SITE FOR RESIDUE HEM A1418
3	AC3	SOFTWARE	LEU A:252 , VAL A:303 , VAL A:404 , HEM A:1418 , HOH A:2197 , HOH A:2383	BINDING SITE FOR RESIDUE GOL A1419
4	AC4	SOFTWARE	HEM B:1418 , HOH B:2151 , HOH B:2304 , HOH B:2307	BINDING SITE FOR RESIDUE GOL B1419

(no "SS Bond" information available for 4C9M)

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	Val B:90	-	Pro B:91
5	Val B:101	-	Pro B:102
6	Pro B:107	-	Pro B:108

(no "SAP(SNP)/Variant" information available for 4C9M)

(no "PROSITE Motif" information available for 4C9M)

(no "Exon" information available for 4C9M)

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 d4c9ma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhh..........hhhhhhhhhhhhhh......eeee.....eeee.hhhhhhhhhh....ee......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....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
                 4c9m 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:407
 aligned with Q2GB12_NOVAD | Q2GB12 from UniProtKB/TrEMBL  Length:421

    Alignment length:407
                                    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       
         Q2GB12_NOVAD    11 KHRVAPPPHVPGHLIREIDAYDLDGLEQGFHEAWKRVQQPDTPPLVWTPFTGGHWIATRGTLIDEIYRSPERFSSRVIWVPREAGEAYDMVPTKLDPPEHTPYRKAIDKGLNLAEIRKLEDQIRTIAVEIIEGFADRGHCEFGSEFSTVFPVRVFLALAGLPVEDATKLGLLANEMTRPSGNTPEEQGRSLEAANKGFFEYVAPIIAARRGGSGTDLITRILNVEIDGKPMPDDRALGLVSLLLLGGLDTVVNFLGFMMIYLSRHPETVAEMRREPLKLQRGVEELFRRFAVVSDARYVVSDMEFHGTMLKEGDLILLPTALHGLDDRHHDDPMTVDLSRRDVTHSTFAQGPHRCAGMHLARLEVTVMLQEWLARIPEFRLKDRAVPIYHSGIVAAVENIPLEWEPQ 417
               SCOP domains d4c9mb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhh..........hhhhhhhhhhhhhh......eeee.....eeee.hhhhhhhhhh....ee......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.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
                 4c9m B  11 KHRVAPPPHVPGHLIREIDAYDLDGLEQGFHEAWKRVQQPDTPPLVWTPFTGGHWIATRGTLIDEIYRSPERFSSRVIWVPREAGEAYDMVPTKLDPPEHTPYRKAIDKGLNLAEIRKLEDQIRTIAVEIIEGFADRGHCEFGSEFSTVFPVRVFLALAGLPVEDATKLGLLANEMTRPSGNTPEEQGRSLEAANKGFFEYVAPIIAARRGGSGTDLITRILNVEIDGKPMPDDRALGLVSLLLLGGLDTVVNFLGFMMIYLSRHPETVAEMRREPLKLQRGVEELFRRFAVVSDARYVVSDMEFHGTMLKEGDLILLPTALHGLDDRHHDDPMTVDLSRRDVTHSTFAQGPHRCAGMHLARLEVTVMLQEWLARIPEFRLKDRAVPIYHSGIVAAVENIPLEWEPQ 417
                                    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

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	d4c9ma_	A:
1b	d4c9mb_	B:

(no "CATH Domain" information available for 4C9M)

(no "Pfam Domain" information available for 4C9M)

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
		Pro A:107 - Pro A:108	[ RasMol ]
		Pro B:107 - Pro B:108	[ 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 ]

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

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	Q2GB12_NOVAD \| Q2GB12	:	3lxh 3lxi 4c9k 4c9l 4c9n 4c9o 4c9p

4c9k	STRUCTURE OF CAMPHOR AND HYDROXYCAMPHOR BOUND WILD TYPE CYP101D1
4c9l	STRUCTURE OF CYANIDE AND CAMPHOR BOUND WILD TYPE CYP101D1
4c9n	STRUCTURE OF CAMPHOR AND HYDROXYCAMPHOR BOUND D259N MUTANT OF CYP101D1
4c9o	STRUCTURE OF CYANIDE AND CAMPHOR BOUND D259N MUTANT OF CYP101D1
4c9p	STRUCTURE OF CAMPHOR BOUND T260A MUTANT OF CYP101D1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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