4G3R - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NITROSYL CYTOCHROME P450CAM

Authors :   Y. Madrona, S. M. Tripathi, H. Li, T. L. Poulos

Date :   15 Jul 12 (Deposition) - 01 Aug 12 (Release) - 05 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   P450, Heme, Monooxygenase, Putidaredoxin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Madrona, S. Tripathi, H. Li, T. L. Poulos
Crystal Structures Of Substrate-Free And Nitrosyl Cytochrom P450Cin: Implications For O(2) Activation.
Biochemistry V. 51 6623 2012
PubMed-ID: 22775403 | Reference-DOI: 10.1021/BI300666U

Molecule 1 - CAMPHOR 5-MONOOXYGENASE
	Chains	:	A, B
	EC Number	:	1.14.15.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCWORI-P450CAM
	Expression System Strain	:	DH5-ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CAMC, CYP101
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Synonym	:	CYTOCHROME P450-CAM, CYTOCHROME P450CAM

		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 (4, 7)

No.	Name	Count	Type	Full Name
1	CAM	2	Ligand/Ion	CAMPHOR
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	2	Ligand/Ion	POTASSIUM ION
4	NO	1	Ligand/Ion	NITRIC OXIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CAM	1	Ligand/Ion	CAMPHOR
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NO	-1	Ligand/Ion	NITRIC OXIDE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CAM	1	Ligand/Ion	CAMPHOR
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	K	-1	Ligand/Ion	POTASSIUM ION
4	NO	-1	Ligand/Ion	NITRIC OXIDE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:100 , THR A:101 , GLN A:108 , ARG A:112 , VAL A:119 , LEU A:244 , LEU A:245 , GLY A:248 , THR A:252 , ASP A:297 , ARG A:299 , GLN A:322 , THR A:349 , PHE A:350 , GLY A:351 , HIS A:355 , CYS A:357 , GLY A:359 , ALA A:363 , CAM A:502 , HOH A:608 , HOH A:678	BINDING SITE FOR RESIDUE HEM A 501
2	AC2	SOFTWARE	PHE A:87 , TYR A:96 , LEU A:244 , HEM A:501	BINDING SITE FOR RESIDUE CAM A 502
3	AC3	SOFTWARE	GLU A:84 , GLY A:93 , GLU A:94 , TYR A:96 , HOH A:758 , HOH A:841	BINDING SITE FOR RESIDUE K A 503
4	AC4	SOFTWARE	PRO B:100 , THR B:101 , GLN B:108 , ARG B:112 , VAL B:119 , LEU B:244 , GLY B:248 , THR B:252 , LEU B:294 , VAL B:295 , ASP B:297 , ARG B:299 , GLN B:322 , THR B:349 , PHE B:350 , GLY B:351 , HIS B:355 , CYS B:357 , GLY B:359 , NO B:504 , HOH B:636	BINDING SITE FOR RESIDUE HEM B 501
5	AC5	SOFTWARE	PHE B:87 , TYR B:96 , VAL B:247 , NO B:504	BINDING SITE FOR RESIDUE CAM B 502
6	AC6	SOFTWARE	GLU B:84 , GLY B:93 , GLU B:94 , TYR B:96 , HOH B:713 , HOH B:765	BINDING SITE FOR RESIDUE K B 503
7	AC7	SOFTWARE	GLY B:248 , THR B:252 , HEM B:501 , CAM B:502	BINDING SITE FOR RESIDUE NO B 504

(no "SS Bond" information available for 4G3R)

Asymmetric Unit

No.	Residues
1	Ile A:88	-	Pro A:89
2	Ile A:99	-	Pro A:100
3	Pro A:105	-	Pro A:106
4	Ile B:88	-	Pro B:89
5	Ile B:99	-	Pro B:100
6	Pro B:105	-	Pro B:106

(no "SAP(SNP)/Variant" information available for 4G3R)

(no "PROSITE Motif" information available for 4G3R)

(no "Exon" information available for 4G3R)

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 d4g3ra_ A: Cytochrome P450-CAM                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh.........hhhhhhhhhhhhhhh.....eeeehhhhheeee.hhhhhhhhhhh...ee......hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeee...eee..eee....eeee..hhhhhh..............................hhhhhhhhhhhhhhhhhh.....ee.......ee.....ee...eee.hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g3r A   8 NANLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPDGSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRILTSDYEFHGVQLKKGDQILLPQMLSGLDERENAAPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREIIVTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPATTKAV 414
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407

Chain B from PDB  Type:PROTEIN  Length:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4g3rb_ B: Cytochrome P450-CAM                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.........hhhhhhhhhhhhhh......eeeehhhhheeee.hhhhhhhhhhh...ee......hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeee...eee..eee....eeee..hhhhhh.......................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee.......ee.....ee...eee.hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g3r B  10 NLAPLPPHVPEHLVFDFDMYNPSNLSAGVQEAWAVLQESNVPDLVWTRCNGGHWIATRGQLIREAYEDYRHFSSECPFIPREAGEAYDFIPTSMDPPEQRQFRALANQVVGMPVVDKLENRIQELACSLIESLRPQGQCNFTEDYAEPFPIRIFMLLAGLPEEDIPHLKYLTDQMTRPDGSMTFAEAKEALYDYLIPIIEQRRQKPGTDAISIVANGQVNGRPITSDEAKRMCGLLLVGGLDTVVNFLSFSMEFLAKSPEHRQELIERPERIPAACEELLRRFSLVADGRILTSDYEFHGVQLKKGDQILLPQMLSGLDERENAAPMHVDFSRQKVSHTTFGHGSHLCLGQHLARREIIVTLKEWLTRIPDFSIAPGAQIQHKSGIVSGVQALPLVWDPATTKAV 414
                                    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

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: Cytochrome P450 (323)

Protein domain: Cytochrome P450-CAM (108)

Pseudomonas putida [TaxId: 303] (108)

1a	d4g3ra_	A:
1b	d4g3rb_	B:

(no "CATH Domain" information available for 4G3R)

(no "Pfam Domain" information available for 4G3R)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CAM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:88 - Pro A:89	[ RasMol ]
		Ile A:99 - Pro A:100	[ RasMol ]
		Ile B:88 - Pro B:89	[ RasMol ]
		Ile B:99 - Pro B:100	[ RasMol ]
		Pro A:105 - Pro A:106	[ RasMol ]
		Pro B:105 - Pro B:106	[ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4g3r
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CPXA_PSEPU \| P00183
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.14.15.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CPXA_PSEPU \| P00183
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

4fb2	P450CIN SUBSTRATE-FREE
4fmx	P450CIN SUBSTRATE-BOUND
4fyz	P450CIN NO-BOUND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File