1GYO - JenaLib

Title :   CRYSTAL STRUCTURE OF THE DI-TETRAHEME CYTOCHROME C3 FROM DESULFOVIBRIO GIGAS AT 1.2 ANGSTROM RESOLUTION

Authors :   D. Aragao, C. Frazao, L. Sieker, G. M. Sheldrick, J. Legall, M. A. Carron

Date :   29 Apr 02 (Deposition) - 24 May 02 (Release) - 29 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Electron Transport, Cytochrome C3, Di-Tetraheme, Ab Initio, Electron Transfer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Aragao, C. Frazao, L. Sieker, G. M. Sheldrick, J. Legall, M. A. Carrondo
Structure Of Dimeric Cytochrome C3 From Desulfovibrio Gigas At 1. 2 A Resolution
Acta Crystallogr. , Sect. D V. 59 644 2003
PubMed-ID: 12657783 | Reference-DOI: 10.1107/S090744490300194X
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:1 , MET A:26 , HIS A:28 , HIS A:31 , VAL A:34 , SER A:35 , CYS A:36 , CYS A:39 , HIS A:40 , PHE A:49 , LYS A:51 , CYS A:52 , HEC A:113 , HOH A:2122 , HOH A:2123 , HOH A:2124 , HOH A:2125 , HOH A:2126 , PHE B:43	BINDING SITE FOR RESIDUE HEC A 111
02	AC2	SOFTWARE	CYS A:39 , HIS A:40 , HIS A:41 , MET A:42 , GLN A:50 , CYS A:52 , CYS A:55 , HIS A:56 , GLU A:65 , ARG A:66 , LYS A:70 , ALA A:71 , SER A:74 , ILE A:78 , SER A:79 , HOH A:2127 , HOH A:2128 , HOH A:2129 , HOH A:2130 , HOH A:2131 , ARG B:20 , LEU B:100	BINDING SITE FOR RESIDUE HEC A 112
03	AC3	SOFTWARE	ILE A:9 , LYS A:30 , HIS A:31 , CYS A:39 , GLU A:77 , ILE A:78 , SER A:79 , CYS A:80 , CYS A:83 , HIS A:84 , MET A:87 , GLN A:93 , THR A:94 , GLY A:95 , PRO A:96 , HEC A:111 , HOH A:2132 , HOH A:2133 , HOH A:2134 , HOH A:2136	BINDING SITE FOR RESIDUE HEC A 113
04	AC4	SOFTWARE	ILE A:9 , HIS A:18 , PHE A:21 , GLY A:22 , LYS A:23 , VAL A:24 , ARG A:59 , ARG A:62 , PHE A:68 , TYR A:69 , TRP A:72 , HIS A:73 , CYS A:80 , ARG A:81 , HIS A:84 , PRO A:96 , ILE A:97 , GLY A:98 , CYS A:99 , CYS A:103 , HIS A:104 , HOH A:2137 , HOH A:2138 , HOH A:2139 , GLN B:50	BINDING SITE FOR RESIDUE HEC A 114
05	AC5	SOFTWARE	LEU A:1 , ASP B:2 , VAL B:3 , ILE B:9 , MET B:26 , HIS B:28 , HIS B:31 , VAL B:34 , SER B:35 , CYS B:36 , CYS B:39 , HIS B:40 , PHE B:49 , LYS B:51 , CYS B:52 , HEC B:113 , HOH B:2127 , HOH B:2128 , HOH B:2129 , HOH B:2130 , HOH B:2131	BINDING SITE FOR RESIDUE HEC B 111
06	AC6	SOFTWARE	ARG A:20 , LEU A:100 , CYS B:39 , HIS B:40 , HIS B:41 , MET B:42 , CYS B:52 , CYS B:55 , HIS B:56 , GLU B:65 , ARG B:66 , LYS B:70 , ALA B:71 , SER B:74 , ILE B:78 , SER B:79 , GOL B:115 , HOH B:2132 , HOH B:2133	BINDING SITE FOR RESIDUE HEC B 112
07	AC7	SOFTWARE	LYS B:30 , HIS B:31 , CYS B:39 , ILE B:78 , SER B:79 , CYS B:80 , CYS B:83 , HIS B:84 , MET B:87 , THR B:94 , GLY B:95 , PRO B:96 , HEC B:111 , HOH B:2134 , HOH B:2135	BINDING SITE FOR RESIDUE HEC B 113
08	AC8	SOFTWARE	GLN A:50 , ILE B:9 , ALA B:11 , PHE B:21 , GLY B:22 , LYS B:23 , VAL B:24 , ARG B:59 , PHE B:68 , TYR B:69 , TRP B:72 , HIS B:73 , CYS B:80 , ARG B:81 , HIS B:84 , PRO B:96 , ILE B:97 , GLY B:98 , CYS B:99 , CYS B:103 , HIS B:104 , HOH B:2025 , HOH B:2136 , HOH B:2137	BINDING SITE FOR RESIDUE HEC B 114
09	AC9	SOFTWARE	PHE A:21 , ARG A:62 , MET B:42 , GLN B:50 , HEC B:112 , GOL B:116 , HOH B:2064 , HOH B:2067 , HOH B:2069 , HOH B:2138	BINDING SITE FOR RESIDUE GOL B 115
10	BC1	SOFTWARE	CYS A:5 , HIS A:18 , ARG A:32 , ARG A:62 , ASP B:44 , CYS B:46 , GOL B:115 , HOH B:2139 , HOH B:2140 , HOH B:2141	BINDING SITE FOR RESIDUE GOL B 116

SS Bonds (2, 2)

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:106
 aligned with Q9R638_DESGI | Q9R638 from UniProtKB/TrEMBL  Length:109

    Alignment length:106
                                    10        20        30        40        50        60        70        80        90       100      
         Q9R638_DESGI     1 LDVPCKVVITAPEGEDPHPRFGKVEMSHAKHRNVSCVSCHHMFDGCGDFQKCADCHIDRDDRSYERGFYKAWHSESEISCRGCHKAMKAKNEQTGPIGCLQGCHEA 106
               SCOP domains d1gyoa_ A: Cytochrome c3                                                                                   SCOP domains
               CATH domains 1gyoA00 A:1-106 Cytochrome C3                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eee.eeeee..............eeeee......hhhhhh.....eeee.hhhhh...........hhhhhhh.....hhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1gyo A   1 LDVPCKVVITAPEGEDPHPRFGKVEMSHAKHRNVSCVSCHHMFDGCGDFQKCADCHIDRDDRSYERGFYKAWHSESEISCRGCHKAMKAKNEQTGPIGCLQGCHEA 106
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with Q9R638_DESGI | Q9R638 from UniProtKB/TrEMBL  Length:109

    Alignment length:106
                                    10        20        30        40        50        60        70        80        90       100      
         Q9R638_DESGI     1 LDVPCKVVITAPEGEDPHPRFGKVEMSHAKHRNVSCVSCHHMFDGCGDFQKCADCHIDRDDRSYERGFYKAWHSESEISCRGCHKAMKAKNEQTGPIGCLQGCHEA 106
               SCOP domains d1gyob_ B: Cytochrome c3                                                                                   SCOP domains
               CATH domains 1gyoB00 B:1-106 Cytochrome C3                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eeeeee............eeeeee......hhhhhh......eee.hhhhh...........hhhhhhhh....hhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1gyo B   1 LDVPCKVVITAPEGEDPHPRFGKVEMSHAKHRNVSCVSCHHMFDGCGDFQKCADCHIDRDDRSYERGFYKAWHSESEISCRGCHKAMKAKNEQTGPIGCLQGCHEA 106
                                    10        20        30        40        50        60        70        80        90       100

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, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q9R638_DESGI | Q9R638)


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.

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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEC	[ 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 ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1gyo)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1gyo
		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
	Q9R638_DESGI \| Q9R638
		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

Description