3H34 - JenaLib

Title :   PPCE, A CYTOCHROME C7 FROM GEOBACTER SULFURREDUCENS

Authors :   P. R. Pokkuluri, M. Schiffer

Date :   15 Apr 09 (Deposition) - 29 Dec 09 (Release) - 28 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Cytochrome C7, Multiheme Cytochrome, Geobacter Sulfurreducens, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. R. Pokkuluri, Y. Y. Londer, X. Yang, N. E. Duke, J. Erickson, V. Orshonsky, G. Johnson, M. Schiffer
Structural Characterization Of A Family Of Cytochromes C(7) Involved In Fe(Iii) Respiration By Geobacter Sulfurreducens.
Biochim. Biophys. Acta V. 1797 222 2010
PubMed-ID: 19857457 | Reference-DOI: 10.1016/J.BBABIO.2009.10.007

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:15 , HIS A:17 , VAL A:24 , CYS A:27 , CYS A:30 , HIS A:31 , PRO A:35 , LYS A:37 , ILE A:38 , PHE A:41 , HOH A:140 , HOH A:149 , HOH A:152 , HOH A:174	BINDING SITE FOR RESIDUE HEM A 72
2	AC2	SOFTWARE	VAL A:13 , PHE A:15 , THR A:16 , ARG A:19 , HIS A:20 , PHE A:23 , VAL A:24 , CYS A:30 , LYS A:48 , THR A:49A , CYS A:51 , CYS A:54 , HIS A:55 , GLY A:61 , PRO A:62 , HOH A:102 , HOH A:106 , HOH A:110 , HOH A:135 , HOH A:148	BINDING SITE FOR RESIDUE HEM A 73
3	AC3	SOFTWARE	SER A:8 , LYS A:9 , ASN A:10 , PHE A:41 , GLY A:42 , ALA A:46 , HIS A:47 , HIS A:55 , PRO A:62 , THR A:63 , CYS A:65 , CYS A:68 , HIS A:69 , HOH A:134 , HOH A:197	BINDING SITE FOR RESIDUE HEM A 74

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

Asymmetric/Biological 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:70
 aligned with Q74CB4_GEOSL | Q74CB4 from UniProtKB/TrEMBL  Length:90

    Alignment length:70
                                    30        40        50        60        70        80        90
         Q74CB4_GEOSL    21 ADVILFPSKNGAVTFTHKRHSEFVRECRSCHEKTPGKIRNFGKDYAHKTCKGCHEVRGAGPTKCKLCHTG  90
               SCOP domains d3h34a_ A: automated matches                                           SCOP domains
               CATH domains 3h34A00 A:1-71 Cytochrome C3                                           CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......eeehhhhhh....hhhhh...........hhhhhhhhhhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 3h34 A   1 ADVILFPSKNGAVTFTHKRHSEFVRECRSCHEKTPGKIRNFGKDYAHKTCKGCHEVRGAGPTKCKLCHTG  71
                                    10        20        30        40        51        61        71
                                                                          49A|                    
                                                                            51

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q74CB4_GEOSL | Q74CB4)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	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.
biological process
	GO:0006791	sulfur utilization	A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary sulfur sources and then activates genes to scavenge the last traces of the primary sulfur source and to transport and metabolize alternate sulfur sources. The utilization process begins when the cell or organism detects sulfur levels, includes the activation of genes whose products detect, transport or metabolize sulfur-containing compounds, and ends when the sulfur is incorporated into the cell or organism's metabolism.

Visualization

Interactive Views

Asymmetric/Biological 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
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3h34)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - 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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3h34
		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
	Q74CB4_GEOSL \| Q74CB4
		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

Analysis Tools

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
	Q74CB4_GEOSL \| Q74CB4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description