2DS5 - JenaLib

Title :   STRUCTURE OF THE ZBD IN THE ORTHORHOMIBIC CRYSTAL FROM

Authors :   H. K. Song, E. Y. Park, B. G. Lee, S. B. Hong

Date :   22 Jun 06 (Deposition) - 13 Feb 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Treble Cleft Zinc Finger, Metal Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Y. Park, B. G. Lee, S. B. Hong, H. W. Kim, H. Jeon, H. K. Song
Structural Basis Of Sspb-Tail Recognition By The Zinc Binding Domain Of Clpx.
J. Mol. Biol. V. 367 514 2007
PubMed-ID: 17258768 | Reference-DOI: 10.1016/J.JMB.2007.01.003
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

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:43
 aligned with CLPX_ECOLI | P0A6H1 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:43
                                    19        29        39        49   
            CLPX_ECOLI   10 GKLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREEI 52
               SCOP domains d2ds5a_ A: automated matches                SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ..................eee....eeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                  2ds5 A  9 GKLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREEI 51
                                    18        28        38        48

Chain B from PDB  Type:PROTEIN  Length:44
 aligned with CLPX_ECOLI | P0A6H1 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:44
                                    18        28        38        48    
            CLPX_ECOLI    9 SGKLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREEI 52
               SCOP domains d2ds5b_ B: automated matches                 SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author ...................eeee..eeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                  2ds5 B  8 SGKLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREEI 51
                                    17        27        37        47

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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CLPX_ECOLI | P0A6H1)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004176	ATP-dependent peptidase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the hydrolysis of peptide bonds.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0051704	multi-organism process	A biological process which involves another organism of the same or different species.
	GO:0030163	protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0043335	protein unfolding	The process of assisting in the disassembly of non-covalent linkages in a protein or protein aggregate, often where the proteins are in a non-functional or denatured state.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.

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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PG4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ds5)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2ds5
		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
	CLPX_ECOLI \| P0A6H1
		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