3NC5 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CYP134A1 STRUCTURE WITH AN OPEN SUBSTRATE BINDING LOOP

Authors :   M. J. Cryle, I. Schlichting

Date :   04 Jun 10 (Deposition) - 11 Aug 10 (Release) - 22 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Cytochrome P450 Oxidase, Haem Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Cryle, S. G. Bell, I. Schlichting
Structural And Biochemical Characterization Of The Cytochrome P450 Cypx (Cyp134A1) From Bacillus Subtilis: A Cyclo-L-Leucyl-L-Leucyl Dipeptide Oxidase.
Biochemistry V. 49 7282 2010
PubMed-ID: 20690619 | Reference-DOI: 10.1021/BI100910Y

Molecule 1 - CYTOCHROME P450 CYPX
	Chains	:	A, B
	EC Number	:	1.14.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A(+)
	Expression System Strain	:	BL21(DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BSU35060, CYP134, CYPB, CYPX
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168

		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, 7)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	MG	3	Ligand/Ion	MAGNESIUM ION

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
3	MG	-1	Ligand/Ion	MAGNESIUM ION

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
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:64 , ASN A:229 , ALA A:233 , ALA A:234 , PRO A:237 , THR A:241 , ARG A:285 , ALA A:345 , PHE A:346 , HIS A:351 , CYS A:353 , GLY A:355 , PHE A:358 , GOL A:407 , HOH A:427	BINDING SITE FOR RESIDUE HEM A 406
2	AC2	SOFTWARE	PRO A:237 , VAL A:280 , TYR A:391 , HEM A:406 , HOH A:427	BINDING SITE FOR RESIDUE GOL A 407
3	AC3	SOFTWARE	ASP A:163 , THR A:166 , SER A:167	BINDING SITE FOR RESIDUE MG A 408
4	AC4	SOFTWARE	GLN A:281 , MET A:307 , ILE A:308 , GLY A:309	BINDING SITE FOR RESIDUE MG A 409
5	AC5	SOFTWARE	GLU B:66 , ILE B:97 , ASN B:229 , ALA B:233 , ALA B:234 , PRO B:237 , LEU B:274 , ILE B:283 , ARG B:285 , ALA B:345 , PHE B:346 , HIS B:351 , CYS B:353 , GLU B:362 , ILE B:363 , HOH B:422	BINDING SITE FOR RESIDUE HEM B 406
6	AC6	SOFTWARE	ALA B:233 , PRO B:237 , TYR B:391 , HOH B:422	BINDING SITE FOR RESIDUE GOL B 407
7	AC7	SOFTWARE	ILE B:97 , VAL B:354 , GLY B:355 , THR B:356 , ALA B:357 , PHE B:358	BINDING SITE FOR RESIDUE MG B 408

(no "SS Bond" information available for 3NC5)

Asymmetric Unit

No.	Residues
1	Ile A:38	-	Asp A:39
2	Ser A:211	-	Glu A:212
3	Ile B:38	-	Asp B:39
4	Val B:65	-	Glu B:66
5	Arg B:90	-	Ile B:91
6	Ser B:211	-	Glu B:212

(no "SAP(SNP)/Variant" information available for 3NC5)

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.	CYPX_BACSU	346-355	2	A:346-355 B:346-355

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.	CYPX_BACSU	346-355	1	A:346-355 -

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.	CYPX_BACSU	346-355	1	- B:346-355

(no "Exon" information available for 3NC5)

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:384
 aligned with CYPX_BACSU | O34926 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:398
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395        
           CYPX_BACSU     6 KLFSVLSDQFQNNPYAYFSQLREEDPVHYEESIDSYFISRYHDVRYILQHPDIFTTKSLVERAEPVMRGPVLAQMHGKEHSAKRRIVVRSFIGDALDHLSPLIKQNAENLLAPYLERGKSDLVNDFGKTFAVCVTMDMLGLDKRDHEKISEWHSGVADFITSISQSPEARAHSLWCSEQLSQYLMPVIKERRVNPGSDLISILCTSEYEGMALSDKDILALILNVLLAATEPADKTLALMIYHLLNNPEQMNDVLADRSLVPRAIAETLRYKPPVQLIPRQLSQDTVVGGMEIKKDTIVFCMIGAANRDPEAFEQPDVFNIHREDLGIKSAFSGAARHLAFGSGIHNCVGAAFAKNEIEIVANIVLDKMRNIRLEEDFCYAESGLYTRGPVSLLVAFD 403
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh.eee.....eeee.hhhhhhhhhhh...ee.............------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...--...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeeee...eee..eee....eeeeehhhhhh..................hhhhh..................hhhhhhhhhhhhhhhhhhhh...ee.......ee.....ee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nc5 A   6 KLFSVLSDQFQNNPYAYFSQLREEDPVHYEESIDSYFISRYHDVRYILQHPDIFTTKSLVERAEPVMR------------SAKRRIVVRSFIGDALDHLSPLIKQNAENLLAPYLERGKSDLVNDFGKTFAVCVTMDMLGLDKRDHEKISEWHSGVADFITSISQSPEARAHSLWCSEQLSQYLMPVIKERRVNPGSDLISILCTSEY--MALSDKDILALILNVLLAATEPADKTLALMIYHLLNNPEQMNDVLADRSLVPRAIAETLRYKPPVQLIPRQLSQDTVVGGMEIKKDTIVFCMIGAANRDPEAFEQPDVFNIHREDLGIKSAFSGAARHLAFGSGIHNCVGTAFAKNEIEIVANIVLDKMRNIRLEEDFCYAESGLYTRGPVSLLVAFD 403
                                    15        25        35        45        55        65       | -         -|       95       105       115       125       135       145       155       165       175       185       195       205       | -|      225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395        
                                                                                              73           86                                                                                                                            213  |                                                                                                                                                                                           
                                                                                                                                                                                                                                            216

Chain B from PDB  Type:PROTEIN  Length:373
 aligned with CYPX_BACSU | O34926 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:398
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395        
           CYPX_BACSU     6 KLFSVLSDQFQNNPYAYFSQLREEDPVHYEESIDSYFISRYHDVRYILQHPDIFTTKSLVERAEPVMRGPVLAQMHGKEHSAKRRIVVRSFIGDALDHLSPLIKQNAENLLAPYLERGKSDLVNDFGKTFAVCVTMDMLGLDKRDHEKISEWHSGVADFITSISQSPEARAHSLWCSEQLSQYLMPVIKERRVNPGSDLISILCTSEYEGMALSDKDILALILNVLLAATEPADKTLALMIYHLLNNPEQMNDVLADRSLVPRAIAETLRYKPPVQLIPRQLSQDTVVGGMEIKKDTIVFCMIGAANRDPEAFEQPDVFNIHREDLGIKSAFSGAARHLAFGSGIHNCVGAAFAKNEIEIVANIVLDKMRNIRLEEDFCYAESGLYTRGPVSLLVAFD 403
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) p450-3nc5B01 B:6-380                                                                                                                                                                                                                                                                                                                                                                   ----------------------- Pfam domains (1)
           Pfam domains (2) p450-3nc5B02 B:6-380                                                                                                                                                                                                                                                                                                                                                                   ----------------------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh.eee......eee.hhhhhhhhhhh...ee........---------------------..hhhhhhhhhhhhhhhhhhhhhhhhhh......eee....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh...----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeeee...............eeeeehhhhhh..................hhhhh...........hhhhh..hhhhhhhhhhhhhhhhhhhh...ee.......ee.....ee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nc5 B   6 KLFSVLSDQFQNNPYAYFSQLREEDPVHYEESIDSYFISRYHDVRYILQHPDIFTTKSLVERA---------------------RIVVRSFIGDALDHLSPLIKQNAENLLAPYLERGKSDLVNDFGKTFAVCVTMDMLGLDKRDHEKISEWHSGVADFITSISQSPEARAHSLWCSEQLSQYLMPVIKERRVNPGSDLISILCTSE----ALSDKDILALILNVLLAATEPADKTLALMIYHLLNNPEQMNDVLADRSLVPRAIAETLRYKPPVQLIPRQLSQDTVVGGMEIKKDTIVFCMIGAANRDPEAFEQPDVFNIHREDLGIKSAFSGAARHLAFGSGIHNCVGTAFAKNEIEIVANIVLDKMRNIRLEEDFCYAESGLYTRGPVSLLVAFD 403
                                    15        25        35        45        55        65  |      -         -    |   95       105       115       125       135       145       155       165       175       185       195       205      |  - |     225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395        
                                                                                         68                    90                                                                                                                       212  217

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 3NC5)

(no "CATH Domain" information available for 3NC5)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: p450 (161)

Bacillus subtilis (6)

1a	p450-3nc5B01	B:6-380
1b	p450-3nc5B02	B:6-380

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYPX_BACSU | O34926)

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.
	GO:0016713	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein 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 iron-sulfur protein 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.
	GO:0046148	pigment biosynthetic process	The chemical reactions and pathways resulting in the formation of a pigment, any general or particular coloring matter in living organisms, e.g. melanin.
	GO:0016125	sterol metabolic process	The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg B:90 - Ile B:91	[ RasMol ]
		Ile A:38 - Asp A:39	[ RasMol ]
		Ile B:38 - Asp B:39	[ RasMol ]
		Ser A:211 - Glu A:212	[ RasMol ]
		Ser B:211 - Glu B:212	[ RasMol ]
		Val B:65 - Glu B:66	[ RasMol ]

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	CYPX_BACSU \| O34926	:	3nc3 3nc6 3nc7

Description

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Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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