4QDF - 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 APO KSHA5 AND KSHA1 IN COMPLEX WITH 1,4-30Q-COA FROM R. RHODOCHROUS

Authors :   J. Penfield, L. J. Worrall, N. C. Strynadka, L. D. Eltis

Date :   13 May 14 (Deposition) - 30 Jul 14 (Release) - 01 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.43

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

Keywords :   Mixed Function Oxygenases, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Penfield, L. J. Worrall, N. C. Strynadka, L. D. Eltis
Substrate Specificities And Conformational Flexibility Of 3-Ketosteroid 9 Alpha-Hydroxylases.
J. Biol. Chem. V. 289 25523 2014
PubMed-ID: 25049233 | Reference-DOI: 10.1074/JBC.M114.575886
(for further references see the PDB file header)

Molecule 1 - 3-KETOSTEROID 9ALPHA-HYDROXYLASE OXYGENASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	GJ1158
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	KSHA5
	Organism Scientific	:	RHODOCOCCUS RHODOCHROUS
	Organism Taxid	:	1829

Molecule 2 - 3-KETOSTEROID 9ALPHA-HYDROXYLASE OXYGENASE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	GJ1158
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	KSHA1
	Organism Scientific	:	RHODOCOCCUS RHODOCHROUS
	Organism Taxid	:	1829

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 8)

No.	Name	Count	Type	Full Name
1	30Q	1	Ligand/Ion	S-[2-(PROPANOYLAMINO)ETHYL] (2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-DIMETHYL-3-OXO-6,7,8,9,10,11,12,13,14,15,16,17-DODECAHYDRO-3H-CYCLOPENTA[A]PHENANTHREN-17-YL]PROPANETHIOATE (NON-PREFERRED NAME)
2	FE2	2	Ligand/Ion	FE (II) ION
3	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
4	GOL	1	Ligand/Ion	GLYCEROL
5	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 12)

No.	Name	Count	Type	Full Name
1	30Q	-1	Ligand/Ion	S-[2-(PROPANOYLAMINO)ETHYL] (2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-DIMETHYL-3-OXO-6,7,8,9,10,11,12,13,14,15,16,17-DODECAHYDRO-3H-CYCLOPENTA[A]PHENANTHREN-17-YL]PROPANETHIOATE (NON-PREFERRED NAME)
2	FE2	3	Ligand/Ion	FE (II) ION
3	FES	3	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
4	GOL	3	Ligand/Ion	GLYCEROL
5	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (4, 12)

No.	Name	Count	Type	Full Name
1	30Q	3	Ligand/Ion	S-[2-(PROPANOYLAMINO)ETHYL] (2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-DIMETHYL-3-OXO-6,7,8,9,10,11,12,13,14,15,16,17-DODECAHYDRO-3H-CYCLOPENTA[A]PHENANTHREN-17-YL]PROPANETHIOATE (NON-PREFERRED NAME)
2	FE2	3	Ligand/Ion	FE (II) ION
3	FES	3	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
4	GOL	-1	Ligand/Ion	GLYCEROL
5	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL
6	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:73 , HIS A:75 , MET A:76 , GLY A:78 , CYS A:92 , HIS A:95 , TRP A:97	BINDING SITE FOR RESIDUE FES A 401
2	AC2	SOFTWARE	HIS A:187 , HIS A:192 , ASP A:311 , HOH A:602 , HOH A:621	BINDING SITE FOR RESIDUE FE2 A 402
3	AC3	SOFTWARE	GLU A:236 , THR A:238	BINDING SITE FOR RESIDUE GOL A 403
4	AC4	SOFTWARE	ARG A:30 , GLY A:31 , TRP A:32 , TRP A:135 , VAL A:147 , THR A:148 , PHE A:240 , GLY A:241 , PRO A:242 , GLN A:342 , PHE A:343 , ILE A:350 , GLU A:352	BINDING SITE FOR RESIDUE PG4 A 404
5	AC5	SOFTWARE	HIS B:181 , HIS B:186 , ASP B:305 , HOH B:533	BINDING SITE FOR RESIDUE FE2 B 401
6	AC6	SOFTWARE	CYS B:68 , HIS B:70 , MET B:71 , GLY B:73 , CYS B:87 , HIS B:90 , TRP B:92	BINDING SITE FOR RESIDUE FES B 402
7	AC7	SOFTWARE	ASN B:175 , ILE B:176 , HIS B:186 , GLN B:204 , SER B:229 , MET B:239 , ASP B:241 , LEU B:243 , TYR B:245 , ASP B:305 , HOH B:513 , HOH B:533	BINDING SITE FOR RESIDUE 30Q B 403
8	AC8	SOFTWARE	PHE B:23 , PHE B:47 , ARG B:116 , HIS B:131 , HOH B:564	BINDING SITE FOR RESIDUE PO4 B 404

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

(no "Cis Peptide Bond" information available for 4QDF)

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

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

(no "Exon" information available for 4QDF)

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:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeehhhhh....eeeee..eeeeeee.....eeeee........hhhhheee..eee......eee....eee..............ee.eeee..eeeeee...........................eeeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee...............eeeeeeeee...eeeeeeeee....eeeeeeeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qdf A  25 PTRFARGWHCLGLLRDFQDGKPHSIEAFGTKLVVFADSKGQLNVLDAYCRHMGGDLSRGEVKGDSIACPFHDWRWNGKGKCTDIPYARRVPPIAKTRAWTTLERNGQLYVWNDPQGNPPPEDVTIPEIAGYGTDEWTDWSWKSLRIKGSHCREIVDNVVDMAHFFYIHYSFPRYFKNVFEGHTATQYMHSTGREDVISGTNYDDPNAELRSEATYFGPSYMIDWLESDANGQTIETILINCHYPVSNNEFVLQYGAIVKKLPGVSDEIAAGMAEQFAEGVQLGFEQDVEIWKNKAPIDNPLLSEEDGPVYQLRRWYQQFYVDVEDITEDMTKRFEFEIDTTRAVASWQKEVAENLAKQAE 384
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384

Chain B from PDB  Type:PROTEIN  Length:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.hhhh....eeeee..eeeeeee.....eeeee........hhhhheee..eee......ee.....eee.................eeee..eeeeee...............hhhhhh......eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.......eeeeeeeee...eeeeeeeee....eeeeeeeeeeeeee..eeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qdf B  20 PARFARGWHCLGLAKDFKDGKPHSVHAFGTKLVVWADSNDEIRILDAYCRHMGGDLSQGTVKGDEIACPFHDWRWGGNGRCKNIPYARRVPPIAKTRAWHTLDQDGLLFVWHDPQGNPPPADVTIPRIAGATSDEWTDWVWYTTEVDTNCREIIDNIVDMAHFFYVHYSFPVYFKNVFEGHVASQFMRGQAREDTRMIGSRSDASYFGPSFMIDDLVYEYEGYDVESVLINCHYPVSQDKFVLMYGMIVKKSDRLEGEKALQTAQQFGNFIAKGFEQDIEIWRNKTRIDNPLLCEEDGPVYQLRRWYEQFYVDVEDVAPEMTDRFEFEMDTTRPVAAWMKEVEANIARKAALDTETR 384
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     ||227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       
                                                                                                                                                                                                                             215|                                                                                                                                                                
                                                                                                                                                                                                                              224

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 4QDF)

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

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

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
		30Q	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FE2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FES	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PG4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ 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 ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4qdf)

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
	4qdf
		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
	KSHA1_RHORH \| F1CMX0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	KSHA5_RHORH \| F1CMY8
		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)
	(no 'Enzyme Classificator' available)
		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
	KSHA1_RHORH \| F1CMX0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	KSHA5_RHORH \| F1CMY8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	KSHA5_RHORH \| F1CMY8	:	4qdc 4qdd

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 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