4J6D - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   THE 2.4 A CRYSTAL STRUCTURE OF CYP154C5 FROM NOCARDIA FARCINICA IN COMPLEX WITH TESTOSTERONE

Authors :   K. Herzog, K. M. Hoffmann

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

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 12)

No.	Name	Count	Type	Full Name
1	FMT	4	Ligand/Ion	FORMIC ACID
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	2	Ligand/Ion	POTASSIUM ION
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	TES	2	Ligand/Ion	TESTOSTERONE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	FMT	2	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	TES	1	Ligand/Ion	TESTOSTERONE

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	FMT	2	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	TES	1	Ligand/Ion	TESTOSTERONE

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	FMT	2	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	TES	1	Ligand/Ion	TESTOSTERONE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:91 , PHE A:92 , HIS A:99 , ARG A:103 , ILE A:158 , ALA A:240 , ALA A:244 , GLY A:245 , THR A:248 , LEU A:252 , PRO A:290 , LEU A:294 , ARG A:297 , TYR A:320 , SER A:349 , PHE A:350 , HIS A:355 , CYS A:357 , PRO A:358 , LEU A:362 , ALA A:363 , TES A:503 , HOH A:601	BINDING SITE FOR RESIDUE HEM A 501
02	AC2	SOFTWARE	HIS A:6 , ASP A:8 , HIS A:382 , HIS A:407	BINDING SITE FOR RESIDUE MG A 502
03	AC3	SOFTWARE	MET A:84 , PHE A:179 , GLN A:239 , ALA A:240 , VAL A:291 , GLN A:398 , HEM A:501 , HOH A:696	BINDING SITE FOR RESIDUE TES A 503
04	AC4	SOFTWARE	LEU A:81 , PHE A:180 , VAL A:395 , LEU A:396 , THR A:397 , HOH A:690	BINDING SITE FOR RESIDUE FMT A 504
05	AC5	SOFTWARE	THR A:58	BINDING SITE FOR RESIDUE FMT A 506
06	AC6	SOFTWARE	MET B:91 , PHE B:92 , HIS B:99 , ARG B:103 , ILE B:158 , ALA B:240 , LEU B:241 , ALA B:244 , GLY B:245 , THR B:248 , LEU B:252 , PRO B:290 , LEU B:294 , ARG B:297 , TYR B:320 , SER B:349 , PHE B:350 , HIS B:355 , CYS B:357 , PRO B:358 , GLY B:359 , ALA B:363 , TES B:502 , HOH B:697	BINDING SITE FOR RESIDUE HEM B 501
07	AC7	SOFTWARE	MET B:84 , PHE B:179 , GLN B:239 , ALA B:240 , VAL B:291 , GLN B:398 , HEM B:501 , HOH B:640	BINDING SITE FOR RESIDUE TES B 502
08	AC8	SOFTWARE	HIS B:6 , ASP B:8 , HIS B:382 , HIS B:407	BINDING SITE FOR RESIDUE MG B 503
09	AC9	SOFTWARE	LEU B:81 , PHE B:180 , LEU B:396 , THR B:397 , HOH B:631	BINDING SITE FOR RESIDUE FMT B 504
10	BC1	SOFTWARE	ASP B:86	BINDING SITE FOR RESIDUE K B 505
11	BC2	SOFTWARE	THR B:56 , ASP B:57 , THR B:58	BINDING SITE FOR RESIDUE FMT B 506

Asymmetric Unit

No.	Residues
1	A:4	-	B:4

Asymmetric Unit

No.	Residues
1	Gly A:30	-	Pro A:31
2	Leu A:295	-	Met A:296
3	Gly B:30	-	Pro B:31
4	Leu B:295	-	Met B:296

(no "SAP(SNP)/Variant" information available for 4J6D)

(no "PROSITE Motif" information available for 4J6D)

(no "Exon" information available for 4J6D)

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:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4j6da_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee......hhhhhhhhhhhh..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
                 4j6d A   4 CPHSDTLTIDPMITDLAGETSRLRAAGPLTRIDLLGVPALAVTGHTLARQLLTDTRLVKDINAWSLWQSGTVTRQWPLIGMIDVDRSMFTVDGPEHRRLRIKTTQALTRRRLDALKPTIERYVAELLDDLERAGADGAVVDLKSVFAYPLPMRVISALMGVPSEDQEQLLTWYKAFFSILTPQDERLRVIDEMHGYFTEMVRRKTAEPGDDLTSALIYATDGETPLTEEEVIGNLQALVAAGHETTVSLILTAVRALLSHPEQLRLVRDGEIGWETAIEETLRWDGPVIHLLMRFATEDIDLGDAVIPRGEGVVMSYRAIGRDITVHGADADDFDITRATAARHISFGHGPHICPGAALARLEAAIALPALFTRFPHLHPALPLDQIPNLPVLTQNDLSHFPIHLGR 410
                                    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

Chain B from PDB  Type:PROTEIN  Length:406
                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4j6db_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee......hhhhhhhhhhhh..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
                 4j6d B   4 CPHSDTLTIDPMITDLAGETSRLRAAGPLTRIDLLGVPALAVTGHTLARQLLTDTRLVKDINAWSLWQSGTVTRQWPLIGMIDVDRSMFTVDGPEHRRLRIKTTQALTRRRLDALKPTIERYVAELLDDLERAGADGAVVDLKSVFAYPLPMRVISALMGVPSEDQEQLLTWYKAFFSILTPQDERLRVIDEMHGYFTEMVRRKTAEPGDDLTSALIYADGETPLTEEEVIGNLQALVAAGHETTVSLILTAVRALLSHPEQLRLVRDGEIGWETAIEETLRWDGPVIHLLMRFATEDIDLGDAVIPRGEGVVMSYRAIGRDITVHGADADDFDITRATAARHISFGHGPHICPGAALARLEAAIALPALFTRFPHLHPALPLDQIPNLPVLTQNDLSHFPIHLGR 410
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404      
                                                                                                                                                                                                                                                    222|                                                                                                                                                                                          
                                                                                                                                                                                                                                                     224

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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	d4j6da_	A:
1b	d4j6db_	B:

(no "CATH Domain" information available for 4J6D)

(no "Pfam Domain" information available for 4J6D)

Asymmetric Unit(hide GO term definitions)

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	Cis Peptide Bonds
		Gly A:30 - Pro A:31	[ 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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	Q5YNS8_NOCFA \| Q5YNS8	:	4j6b 4j6c 4jbt

4j6b	CYP154C5 IN COMPLEX WITH PREGNENOLONE
4j6c	CYP154C5 IN COMPLEX WITH PROGESTERONE
4jbt

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 12)

Sites (11, 11)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (7, 7)

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