2CWP - JenaLib

Asymmetric Unit

Biological Unit 1

Biological Unit 2

collapse

expand

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Description

Title :   CRYSTAL STRUCTURE OF METRS RELATED PROTEIN FROM PYROCOCCUS HORIKOSHII

Authors :   K. Murayama, M. Kato-Murayama, M. Shirouzu, S. Yokoyama, Riken Struc Genomics/Proteomics Initiative (Rsgi)

Date :   23 Jun 05 (Deposition) - 23 Dec 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Metrs Related Protein, Pyrococcus Horikoshii, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Nppsfa, National Project On Protein Structural And Functional Analyses, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Murayama, M. Kato-Murayama, M. Shirouzu, S. Yokoyama
Crystal Structure Of Metrs Related Protein From Pyrococcus Horikoshii
To Be Published
PubMed: search

Compounds

Molecule 1 - METRS RELATED PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2CWP)

Sites (0, 0)

(no "Site" information available for 2CWP)

SS Bonds (0, 0)

(no "SS Bond" information available for 2CWP)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2CWP)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2CWP)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 2CWP)

Exons (0, 0)

(no "Exon" information available for 2CWP)

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:109
 aligned with O58023_PYRHO | O58023 from UniProtKB/TrEMBL  Length:112

    Alignment length:109
                                    13        23        33        43        53        63        73        83        93       103         
         O58023_PYRHO     4 MELYDVDEFWKFQMKVGLVKKAEKIKRTKKLIKLIVDFGNEERTIVTGIADQIPPEELEGKKFIFVVNLKPKKFSGVESQGMLILAETEDGKVYLIPVPEEVPVGARVW 112
               SCOP domains d2cwpa_ A: automated matches                                                                                  SCOP domains
               CATH domains 2cwpA00 A:4-112 Nucleic acid-binding proteins                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh..eeeeeeeeeee.......eeeeee....eeeeee......hhhhh...eeeee.....eee..eee..ee..ee.....ee............ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2cwp A   4 MELYDVDEFWKFQMKVGLVKKAEKIKRTKKLIKLIVDFGNEERTIVTGIADQIPPEELEGKKFIFVVNLKPKKFSGVESQGMLILAETEDGKVYLIPVPEEVPVGARVW 112
                                    13        23        33        43        53        63        73        83        93       103

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)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Nucleic acid-binding proteins (590)

Family: automated matches (46)

Protein domain: automated matches (46)

Pyrococcus horikoshii [TaxId: 53953] (4)

d2cwpa_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: Nucleic acid-binding proteins (483)

Pyrococcus horikoshii. Organism_taxid: 53953. (5)

2cwpA00

A:4-112

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2CWP)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (O58023_PYRHO | O58023)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004812	aminoacyl-tRNA ligase activity	Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
	GO:0004825	methionine-tRNA ligase activity	Catalysis of the reaction: ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met).
	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:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0006431	methionyl-tRNA aminoacylation	The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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
(no "Ligands, Modified Residues, Ions" information available for 2cwp)

	Sites
(no "Sites" information available for 2cwp)

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

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

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 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)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2cwp
		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
	O58023_PYRHO \| O58023
		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
	O58023_PYRHO \| O58023
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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