3QNS - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   DYPB FROM RHODOCOCCUS JOSTII RHA1, CRYSTAL FORM 2

Authors :   J. C. Grigg, J. N. Roberts, R. Singh, L. D. Eltis, M. E. P. Murphy

Date :   09 Feb 11 (Deposition) - 27 Apr 11 (Release) - 29 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

Keywords :   Peroxidase, Lignan, Heme, Dyp, Enzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. N. Roberts, R. Singh, J. C. Grigg, M. E. Murphy, T. D. Bugg, L. D. Eltis
Characterization Of Dye-Decolorizing Peroxidases From Rhodococcus Jostii Rha1.
Biochemistry V. 50 5108 2011
PubMed-ID: 21534572 | Reference-DOI: 10.1021/BI200427H

Molecule 1 - DYP PEROXIDASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	DYPB, RHA1_RO02407
	Organism Scientific	:	RHODOCOCCUS JOSTII RHA1
	Organism Taxid	:	101510
	Strain	:	RHA1

		1
Asymmetric Unit	:	A
Biological Unit 1 (6x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 48)

No.	Name	Count	Type	Full Name
1	GOL	30	Ligand/Ion	GLYCEROL
2	HEM	6	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	12	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:147 , PHE A:151 , VAL A:152 , ASP A:153 , GLY A:154 , THR A:155 , GLU A:156 , GLN A:185 , TYR A:187 , HIS A:189 , ARG A:208 , HIS A:226 , VAL A:227 , ASN A:230 , ARG A:244 , PHE A:261 , MET A:274 , LEU A:275 , MET A:278 , SER A:294 , HOH A:406 , HOH A:420 , HOH A:423 , HOH A:473 , HOH A:507 , HOH A:561	BINDING SITE FOR RESIDUE HEM A 351
2	AC2	SOFTWARE	LYS A:113 , HIS A:138 , HOH A:450 , HOH A:466 , HOH A:594 , HOH A:637 , HOH A:639 , HOH A:659	BINDING SITE FOR RESIDUE SO4 A 352
3	AC3	SOFTWARE	GLU A:56 , LEU A:57 , ALA A:58 , ARG A:112 , ARG A:141 , HOH A:378 , HOH A:481 , HOH A:518 , HOH A:688	BINDING SITE FOR RESIDUE SO4 A 353
4	AC4	SOFTWARE	HIS A:240 , PRO A:284 , HOH A:698	BINDING SITE FOR RESIDUE GOL A 354
5	AC5	SOFTWARE	ARG A:121 , LEU A:148 , LEU A:149 , MET A:191 , TRP A:194 , ASN A:195 , LYS A:210 , LEU A:211 , GLU A:212 , HOH A:407 , HOH A:475 , HOH A:700	BINDING SITE FOR RESIDUE GOL A 355
6	AC6	SOFTWARE	PRO A:222 , SER A:223 , ASN A:224 , HOH A:571	BINDING SITE FOR RESIDUE GOL A 356
7	AC7	SOFTWARE	HIS A:189 , ASP A:190 , MET A:191 , SER A:192 , ALA A:255 , TYR A:257 , HOH A:662 , HOH A:744 , HOH A:766	BINDING SITE FOR RESIDUE GOL A 357
8	AC8	SOFTWARE	ASN A:224 , ASN A:286 , TYR A:287 , HOH A:712	BINDING SITE FOR RESIDUE GOL A 358

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

Asymmetric Unit

No.	Residues
1	Glu A:282	-	Pro A:283

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

(no "PROSITE Motif" information available for 3QNS)

(no "Exon" information available for 3QNS)

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:311
 aligned with Q0SE24_RHOJR | Q0SE24 from UniProtKB/TrEMBL  Length:350

    Alignment length:311
                                    14        24        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 
         Q0SE24_RHOJR     5 VARLAPQAVLTPPSAASLFLVLVAGDSDDDRATVCDVISGIDGPLKAVGFRELAGSLSCVVGVGAQFWDRVSASSKPAHLHPFVPLSGPVHSAPSTPGDLLFHIKAARKDLCFELGRQIVSALGSAATVVDEVHGFRYFDSRDLLGFVDGTENPTDDDAADSALIGDEDPDFRGGSYVIVQKYLHDMSAWNTLSTEEQERVIGRTKLENVELDDDAQPSNSHVTLNTIVDDDGVEHDILRDNMAFGSLGEAEYGTYFIGYAKDPAVTELMLRRMFLGEPPGNYDRVLDFSTAATGTLFFVPSRDVLESLGD 315
               SCOP domains d3qnsa_ A: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhh.............ee....ee......eeeeeee.hhhhhhhhhhhhhhhhh..eeeeeeeeee..................hhhhhhhhhh....hhhhh..eeeeeeeeeehhhhhh..hhhhhhhhhh.........hhhhh...hhhhhh.ee.....ee..ee..eeeee....eeeeeeeeee.hhhhhhhhhhhhhhh......hhhhh.eee...eeeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qns A   5 VARLAPQAVLTPPSAASLFLVLVAGDSDDDRATVCDVISGIDGPLKAVGFRELAGSLSCVVGVGAQFWDRVSASSKPAHLHPFVPLSGPVHSAPSTPGDLLFHIKAARKDLCFELGRQIVSALGSAATVVDEVHGFRYFDSRDLLGFVDGTENPTDDDAADSALIGDEDPDFRGGSYVIVQKYLHDMSAWNTLSTEEQERVIGRTKLENVELDDDAQPSNSHVTLNTIVDDDGVEHDILRDNMAFGSLGEAEYGTYFIGYAKDPAVTELMLRRMFLGEPPGNYDRVLDFSTAATGTLFFVPSRDVLESLGD 315
                                    14        24        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

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: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Dimeric alpha+beta barrel (122)

Family: automated matches (41)

Protein domain: automated matches (41)

Rhodococcus jostii [TaxId: 101510] (8)

d3qnsa_

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

(no "Pfam Domain" information available for 3QNS)

Asymmetric Unit(hide GO term definitions)

Chain A (Q0SE24_RHOJR | Q0SE24)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	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.

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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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
		Glu A:282 - Pro A:283	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	3qns
		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
	Q0SE24_RHOJR \| Q0SE24
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	Q0SE24_RHOJR \| Q0SE24
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q0SE24_RHOJR \| Q0SE24	:	3qnr 3vec 3ved 3vee 3vef 3veg 4hov

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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