1X9R - JenaLib

Title :   UMECYANIN FROM HORSE RADDISH- CRYSTAL STRUCTURE OF THE OXIDISED FORM

Authors :   M. Koch, M. Velarde, M. D. Harrison, S. Echt, M. Fischer, A. Messerschmidt, C. Dennison

Date :   24 Aug 04 (Deposition) - 22 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Umecyanin, Cupredoxin, Phytocyanin, Copper Binding Site, Beta Barrel, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Koch, M. Velarde, M. D. Harrison, S. Echt, M. Fischer, A. Messerschmidt, C. Dennison
Crystal Structures Of Oxidized And Reduced Stellacyanin From Horseradish Roots
J. Am. Chem. Soc. V. 127 158 2005
PubMed-ID: 15631465 | Reference-DOI: 10.1021/JA046184P
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_UMEC_ARMRU_001 *	V	48	I	UMEC_ARMRU	---	---	A/B	V	48	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_UMEC_ARMRU_001 *	V	48	I	UMEC_ARMRU	---	---	A	V	48	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_UMEC_ARMRU_001 *	V	48	I	UMEC_ARMRU	---	---	B	V	48	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHYTOCYANIN	PS51485	Phytocyanin domain profile.	UMEC_ARMRU	1-103	2	A:1-103 B:1-103
2	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	UMEC_ARMRU	79-95	2	A:79-95 B:79-95

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHYTOCYANIN	PS51485	Phytocyanin domain profile.	UMEC_ARMRU	1-103	1	A:1-103 -
2	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	UMEC_ARMRU	79-95	1	A:79-95 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHYTOCYANIN	PS51485	Phytocyanin domain profile.	UMEC_ARMRU	1-103	1	- B:1-103
2	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	UMEC_ARMRU	79-95	1	- B:79-95

Exons (0, 0)

Sequences/Alignments

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:105
 aligned with UMEC_ARMRU | P42849 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:105
                             1                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99     
           UMEC_ARMRU     - -EDYDVGGDMEWKRPSDPKFYITWATGKTFRVGDELEFDFAAGMHDVAVVTKDAFDNCKKENPISHMTTPPVKIMLNTTGPQYYICTVGDHCRVGQKLSINVVGA 104
               SCOP domains d1x9ra_ A: automated matches                                                                              SCOP domains
               CATH domains 1x9rA00 A:0-104 Cupredoxins -  blue copper proteins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhh.......hhhhhhhh...ee...eeee........eeeehhhhhhh.......eee....eeee....eeeeee...........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------I-------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PHYTOCYANIN  PDB: A:1-103 UniProt: 1-103                                                               - PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------COPPER_BLUE      --------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1x9r A   0 MEDYDVGGDMEWKRPSDPKFYITWATGKTFRVGDELEFDFAAGMHDVAVVTKDAFDNCKKENPISHMTTPPVKIMLNTTGPQYYICTVGDHCRVGQKLSINVVGA 104
                                     9        19        29        39        49        59        69        79        89        99

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with UMEC_ARMRU | P42849 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:104
                             1                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99    
           UMEC_ARMRU     - -EDYDVGGDMEWKRPSDPKFYITWATGKTFRVGDELEFDFAAGMHDVAVVTKDAFDNCKKENPISHMTTPPVKIMLNTTGPQYYICTVGDHCRVGQKLSINVVG 103
               SCOP domains d1x9rb_ B: automated matches                                                                             SCOP domains
               CATH domains 1x9rB00 B:0-103 Cupredoxins -  blue copper proteins                                                      CATH domains
           Pfam domains (1) -----------Cu_bind_like-1x9rB01 B:11-95                                                         -------- Pfam domains (1)
           Pfam domains (2) -----------Cu_bind_like-1x9rB02 B:11-95                                                         -------- Pfam domains (2)
         Sec.struct. author ..eee.hhhhh.......hhhhhhhh...ee...eeee........eee.hhhhhhh.......eee....eeee....eeeeee...........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------I------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PHYTOCYANIN  PDB: B:1-103 UniProt: 1-103                                                                PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------COPPER_BLUE      -------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1x9r B   0 MEDYDVGGDMEWKRPSDPKFYITWATGKTFRVGDELEFDFAAGMHDVAVVTKDAFDNCKKENPISHMTTPPVKIMLNTTGPQYYICTVGDHCRVGQKLSINVVG 103
                                     9        19        29        39        49        59        69        79        89        99

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 (1, 2)

Gene Ontology (3, 3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (UMEC_ARMRU | P42849)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.

Visualization

Interactive Views

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
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1x9r)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1x9r
		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
	UMEC_ARMRU \| P42849
		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

Description