3PWF - 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 :   HIGH RESOLUTION STRUCTURE OF THE FULLY REDUCED FORM OF RUBRERYTHRIN FROM P. FURIOSUS

Authors :   B. D. Dillard, J. M. Demick, M. W. Adams, W. N. Lanzilotta

Date :   08 Dec 10 (Deposition) - 22 Jun 11 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.64

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

Keywords :   Non Heme Iron Peroxidases, Oxidative Stress, Rubrerythrin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. D. Dillard, J. M. Demick, M. W. Adams, W. N. Lanzilotta
A Cryo-Crystallographic Time Course For Peroxide Reduction By Rubrerythrin From Pyrococcus Furiosus.
J. Biol. Inorg. Chem. V. 16 949 2011
PubMed-ID: 21647777 | Reference-DOI: 10.1007/S00775-011-0795-6

Molecule 1 - RUBRERYTHRIN
	Chains	:	A, B
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	FE2	6	Ligand/Ion	FE (II) ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	FE2	6	Ligand/Ion	FE (II) ION

Biological Unit 2 (1, 12)

No.	Name	Count	Type	Full Name
1	FE2	12	Ligand/Ion	FE (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:142 , CYS A:145 , CYS A:157 , CYS A:160	BINDING SITE FOR RESIDUE FE2 A 200
2	AC2	SOFTWARE	GLU A:80 , GLU A:114 , HIS A:117 , HOH A:176 , HOH A:288 , GLU B:52	BINDING SITE FOR RESIDUE FE2 A 201
3	AC3	SOFTWARE	GLU A:19 , GLU A:52 , HIS A:55 , GLU B:114 , HOH B:172	BINDING SITE FOR RESIDUE FE2 A 202
4	AC4	SOFTWARE	CYS B:142 , CYS B:145 , CYS B:157 , CYS B:160	BINDING SITE FOR RESIDUE FE2 B 200
5	AC5	SOFTWARE	GLU A:52 , GLU B:80 , GLU B:114 , HIS B:117 , HOH B:172 , HOH B:290	BINDING SITE FOR RESIDUE FE2 B 201
6	AC6	SOFTWARE	GLU A:114 , HOH A:176 , GLU B:19 , GLU B:52 , HIS B:55	BINDING SITE FOR RESIDUE FE2 B 202

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

(no "Cis Peptide Bond" information available for 3PWF)

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

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

(no "Exon" information available for 3PWF)

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:170
 aligned with Q9UWP7_9EURY | Q9UWP7 from UniProtKB/TrEMBL  Length:171

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
         Q9UWP7_9EURY     2 VVKRTMTKKFLEEAFAGESMAHMRYLIFAEKAEQEGFPNIAKLFRAIAYAEFVHAKNHFIALGKLGKTPENLQMGIEGETFEVEEMYPVYNKAAEFQGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKEKFVVFE 171
               SCOP domains d3pwfa1 A:2-134 automated matches                                                                                                    d3pwfa2 A:135-171 automated matches   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee......eee............hhhhheee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pwf A   2 VVKRTMTKKFLEEAFAGESMAHMRYLIFAEKAEQEGFPNIAKLFRAIAYAEFVHAKNHFIALGKLGKTPENLQMGIEGETFEVEEMYPVYNKAAEFQGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKEKFVVFE 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with Q9UWP7_9EURY | Q9UWP7 from UniProtKB/TrEMBL  Length:171

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
         Q9UWP7_9EURY     2 VVKRTMTKKFLEEAFAGESMAHMRYLIFAEKAEQEGFPNIAKLFRAIAYAEFVHAKNHFIALGKLGKTPENLQMGIEGETFEVEEMYPVYNKAAEFQGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKEKFVVFE 171
               SCOP domains d3pwfb1 B:2-134 automated matches                                                                                                    d3pwfb2 B:135-171 automated matches   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------Rubrerythrin-3pwfB01 B:10-125                                                                                       ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------Rubrerythrin-3pwfB02 B:10-125                                                                                       ---------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee......eee............hhhhheee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pwf B   2 VVKRTMTKKFLEEAFAGESMAHMRYLIFAEKAEQEGFPNIAKLFRAIAYAEFVHAKNHFIALGKLGKTPENLQMGIEGETFEVEEMYPVYNKAAEFQGEKEAVRTTHYALEAEKIHAELYRKAKEKAEKGEDIEIKKVYICPICGYTAVDEAPEYCPVCGAPKEKFVVFE 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

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: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Ferritin (232)

Protein domain: automated matches (70)

Pyrococcus furiosus [TaxId: 2261] (4)

1a	d3pwfa1	A:2-134
1b	d3pwfb1	B:2-134

Class: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Rubredoxin-like (127)

Family: automated matches (7)

Protein domain: automated matches (7)

Pyrococcus furiosus [TaxId: 2261] (4)

2a	d3pwfa2	A:135-171
2b	d3pwfb2	B:135-171

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Rubrerythrin (18)

Pyrococcus furiosus (5)

1a	Rubrerythrin-3pwfB01	B:10-125
1b	Rubrerythrin-3pwfB02	B:10-125

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9UWP7_9EURY | Q9UWP7)

molecular function
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	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
		FE2	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pwf)

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
	3pwf
		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
	Q9UWP7_9EURY \| Q9UWP7
		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
	Q9UWP7_9EURY \| Q9UWP7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q9UWP7_9EURY \| Q9UWP7	:	1nnq 2hr5 3mps 3pza 3qvd

(no "Related Entries Specified in the PDB File" available for 3PWF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

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 (2, 4)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (4, 4)

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