4J6B - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   THE 2.2 A CRYSTAL STRUCTURE OF CYP154C5 FROM NOCARDIA FARCINICA IN COMPLEX WITH PREGNENOLONE

Authors :   K. Herzog, K. M. Hoffmann

Date :   11 Feb 13 (Deposition) - 05 Mar 14 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Cytochrom P450, Steroid Hydroxylating Monooxygenase, Steroid Binding, Oxidoreductase-Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Herzog, P. Bracco, A. Onoda, T. Hayashi, K. Hoffmann, A. Schallmey
Enzyme-Substrate Complex Structures Of Cyp154C5 Shed Light On Its Mode Of Highly Selective Steroid Hydroxylation.
Acta Crystallogr. , Sect. D V. 70 2875 2014
PubMed-ID: 25372679 | Reference-DOI: 10.1107/S1399004714019129

Molecule 1 - CYTOCHROME P450 MONOOXYGENASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	C43 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NFA_53110
	Organism Scientific	:	NOCARDIA FARCINICA
	Organism Taxid	:	247156
	Strain	:	IFM 10152

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 11)

No.	Name	Count	Type	Full Name
1	FMT	4	Ligand/Ion	FORMIC ACID
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	1	Ligand/Ion	POTASSIUM ION
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	PLO	2	Ligand/Ion	(3BETA)-3-HYDROXYPREGN-5-EN-20-ONE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	PLO	1	Ligand/Ion	(3BETA)-3-HYDROXYPREGN-5-EN-20-ONE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	PLO	1	Ligand/Ion	(3BETA)-3-HYDROXYPREGN-5-EN-20-ONE

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	PLO	1	Ligand/Ion	(3BETA)-3-HYDROXYPREGN-5-EN-20-ONE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:84 , PHE A:179 , GLN A:239 , ALA A:240 , THR A:248 , VAL A:291 , GLN A:398 , HEM A:502 , HOH A:751 , HOH A:779 , HOH A:846	BINDING SITE FOR RESIDUE PLO A 501
02	AC2	SOFTWARE	LEU A:55 , MET A:91 , PHE A:92 , HIS A:99 , ARG A:103 , ILE A:158 , ALA A:244 , GLY A:245 , THR A:248 , THR A:249 , PRO A:290 , LEU A:294 , ARG A:297 , TYR A:320 , SER A:349 , PHE A:350 , GLY A:351 , HIS A:355 , CYS A:357 , PRO A:358 , GLY A:359 , ALA A:363 , PLO A:501 , HOH A:625 , HOH A:682	BINDING SITE FOR RESIDUE HEM A 502
03	AC3	SOFTWARE	HIS A:6 , ASP A:8 , HIS A:382 , HIS A:407	BINDING SITE FOR RESIDUE MG A 503
04	AC4	SOFTWARE	LEU A:81 , PHE A:180 , LEU A:396 , THR A:397 , HOH A:782	BINDING SITE FOR RESIDUE FMT A 504
05	AC5	SOFTWARE	ASP A:88	BINDING SITE FOR RESIDUE K A 505
06	AC6	SOFTWARE	MET B:91 , PHE B:92 , HIS B:99 , ARG B:103 , ILE B:158 , LEU B:241 , ALA B:244 , GLY B:245 , THR B:248 , THR B:249 , PRO B:290 , LEU B:294 , ARG B:297 , TYR B:320 , SER B:349 , PHE B:350 , GLY B:351 , HIS B:355 , CYS B:357 , PRO B:358 , GLY B:359 , ALA B:363 , PLO B:503 , HOH B:653 , HOH B:744	BINDING SITE FOR RESIDUE HEM B 501
07	AC7	SOFTWARE	HIS B:6 , ASP B:8 , HIS B:382 , HIS B:407	BINDING SITE FOR RESIDUE MG B 502
08	AC8	SOFTWARE	GLY B:83 , MET B:84 , PHE B:179 , GLN B:239 , ALA B:240 , THR B:248 , GLN B:398 , HEM B:501 , HOH B:768	BINDING SITE FOR RESIDUE PLO B 503
09	AC9	SOFTWARE	THR B:56 , ASP B:57 , THR B:58 , ARG B:59	BINDING SITE FOR RESIDUE FMT B 504
10	BC1	SOFTWARE	THR A:56 , ASP A:57 , THR A:58 , ARG A:59	BINDING SITE FOR RESIDUE FMT B 505
11	BC2	SOFTWARE	PHE B:180 , LEU B:396 , THR B:397 , HOH B:771	BINDING SITE FOR RESIDUE FMT B 506

(no "SS Bond" information available for 4J6B)

Asymmetric Unit

No.	Residues
1	Gly A:30	-	Pro A:31
2	Glu A:226	-	Thr A:227
3	Leu A:295	-	Met A:296
4	Gly B:30	-	Pro B:31
5	Gly B:225	-	Glu B:226
6	Leu B:295	-	Met B:296

(no "SAP(SNP)/Variant" information available for 4J6B)

(no "PROSITE Motif" information available for 4J6B)

(no "Exon" information available for 4J6B)

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:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4j6ba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee......hhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...ee.hhhhhhhhhh........hhhhh..........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.eehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....eeeeee...ee....ee....eeeehhhhhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6b A   4 CPHSDTLTIDPMITDLAGETSRLRAAGPLTRIDLLGVPALAVTGHTLARQLLTDTRLVKDINAWSLWQSGTVTRQWPLIGMIDVDRSMFTVDGPEHRRLRIKTTQALTRRRLDALKPTIERYVAELLDDLERAGADGAVVDLKSVFAYPLPMRVISALMGVPSEDQEQLLTWYKAFFSILTPQDERLRVIDEMHGYFTEMVRRKTAEPGDDLTSALIYATETPLTEEEVIGNLQALVAAGHETTVSLILTAVRALLSHPEQLRLVRDGEIGWETAIEETLRWDGPVIHLLMRFATEDIDLGDAVIPRGEGVVMSYRAIGRDITVHGADADDFDITRATAARHISFGHGPHICPGAALARLEAAIALPALFTRFPHLHPALPLDQIPNLPVLTQNDLSHFPIHLGR 410
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223|      235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405     
                                                                                                                                                                                                                                                     223|                                                                                                                                                                                        
                                                                                                                                                                                                                                                      226

Chain B from PDB  Type:PROTEIN  Length:406
                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4j6bb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee......hhhhhhhhhhhh..eeeeee..eeeeee.hhhhhhhhh....ee.hhhhhhhhhh........hhhhh..........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.eehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....eeeeee...ee....ee....eeeehhhhhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j6b B   4 CPHSDTLTIDPMITDLAGETSRLRAAGPLTRIDLLGVPALAVTGHTLARQLLTDTRLVKDINAWSLWQSGTVTRQWPLIGMIDVDRSMFTVDGPEHRRLRIKTTQALTRRRLDALKPTIERYVAELLDDLERAGADGAVVDLKSVFAYPLPMRVISALMGVPSEDQEQLLTWYKAFFSILTPQDERLRVIDEMHGYFTEMVRRKTAEPGDDLTSALIYATGETPLTEEEVIGNLQALVAAGHETTVSLILTAVRALLSHPEQLRLVRDGEIGWETAIEETLRWDGPVIHLLMRFATEDIDLGDAVIPRGEGVVMSYRAIGRDITVHGADADDFDITRATAARHISFGHGPHICPGAALARLEAAIALPALFTRFPHLHPALPLDQIPNLPVLTQNDLSHFPIHLGR 410
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223|      234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404      
                                                                                                                                                                                                                                                     223|                                                                                                                                                                                         
                                                                                                                                                                                                                                                      225

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)

Nocardia farcinica [TaxId: 247156] (4)

1a	d4j6ba_	A:
1b	d4j6bb_	B:

(no "CATH Domain" information available for 4J6B)

(no "Pfam Domain" information available for 4J6B)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:226 - Thr A:227	[ RasMol ]
		Gly A:30 - Pro A:31	[ RasMol ]
		Gly B:225 - Glu B:226	[ RasMol ]
		Gly B:30 - Pro B:31	[ RasMol ]
		Leu A:295 - Met A:296	[ RasMol ]
		Leu B:295 - Met B:296	[ RasMol ]

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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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SAPs(SNPs)/Variants (0, 0)

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