2O4T - JenaLib

Biol.Unit 1 - manually

Asym.Unit - manually

Asymmetric Unit

Asym. Unit - sites

Biological Unit 1

Biol. Unit 1 - sites

collapse

expand

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Description

Title :   CRYSTAL STRUCTURE OF A PROTEIN OF THE DUF1048 FAMILY WITH A LEFT-HANDED SUPERHELIX FOLD (BH3976) FROM BACILLUS HALODURANS AT 1.95 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   04 Dec 06 (Deposition) - 26 Dec 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Left-Handed Superhelix Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Bh3976 (10176601) From Bacillus Halodurans At 1. 95 A Resolution
To Be Published
PubMed: search

Compounds

Molecule 1 - BH3976 PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 15-113
	Gene	:	10176601
	Organism Scientific	:	BACILLUS HALODURANS
	Organism Taxid	:	86665

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:33 , TYR A:37 , VAL A:78 , HOH A:148	BINDING SITE FOR RESIDUE PEG A 1
2	AC2	SOFTWARE	ASP A:72 , VAL A:73 , THR A:74 , PHE A:81	BINDING SITE FOR RESIDUE PEG A 2

SS Bonds (0, 0)

(no "SS Bond" information available for 2O4T)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2O4T)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2O4T)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 2O4T)

Exons (0, 0)

(no "Exon" information available for 2O4T)

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:90
 aligned with Q9K5W1_BACHD | Q9K5W1 from UniProtKB/TrEMBL  Length:113

    Alignment length:90
                                    25        35        45        55        65        75        85        95       105
         Q9K5W1_BACHD    16 HVSRVEKLPKDYQIVYKEIQKYLFKVGPVELNEGIGLLSEILGFFEEGAAAGKGVLDVTGTDVAAFCDALIGDSKTYADLYQESIQQHVD 105
               SCOP domains d2o4ta1 A:16-105 Uncharacterized protein BH3976                                            SCOP domains
               CATH domains 2o4tA00 A:16-105 c-terminal domain of poly(a) binding protein                              CATH domains
               Pfam domains DUF1048-2o4tA01 A:16-105                                                                   Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2o4t A  16 HVSRVEKLPKDYQIVYKEIQKYLFKVGPVELNEGIGLLSEILGFFEEGAAAGKGVLDVTGTDVAAFCDALIGDSKTYADLYQESIQQHVD 105
                                    25        35        45        55        65        75        85        95       105

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 alpha proteins (14657)

Fold: Left-handed superhelix (73)

Superfamily: BH3980-like (3)

Family: BH3980-like (3)

Protein domain: Uncharacterized protein BH3976 (1)

Bacillus halodurans [TaxId: 86665] (1)

d2o4ta1

A:16-105

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: c-terminal domain of poly(a) binding protein (10)

Homologous Superfamily: c-terminal domain of poly(a) binding protein (8)

Bacillus halodurans. Organism_taxid: 86665. (2)

2o4tA00

A:16-105

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Yip1 (2)

Family: DUF1048 (2)

Bacillus halodurans (1)

DUF1048-2o4tA01

A:16-105

Gene Ontology (1, 1)

Asymmetric Unit(hide GO term definitions)

Chain A (Q9K5W1_BACHD | Q9K5W1)

molecular function
	GO:0003723		RNA binding		Interacting selectively and non-covalently with an RNA molecule or a portion thereof.

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

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2o4t)

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	2o4t
		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
	Q9K5W1_BACHD \| Q9K5W1
		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
	Q9K5W1_BACHD \| Q9K5W1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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 (1, 1)

Gene Ontology (1, 1)

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