4ENC - JenaLib

Title :   CRYSTAL STRUCTURE OF FLUORIDE RIBOSWITCH

Authors :   A. M. Ren, K. R. Rajashankar, D. J. Patel

Date :   12 Apr 12 (Deposition) - 09 May 12 (Release) - 13 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.27

Chains :   Asym./Biol. Unit : A

Keywords :   Pseudoknot, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ren, K. R. Rajashankar, D. J. Patel
Fluoride Ion Encapsulation By Mg2+ Ions And Phosphates In A Fluoride Riboswitch.
Nature V. 486 85 2012
PubMed-ID: 22678284 | Reference-DOI: 10.1038/NATURE11152

Compounds

Molecule 1 - FLUORIDE RIBOSWITCH
	Chains	:	A
	Engineered	:	YES
	Organism Scientific	:	THERMOTOGA PETROPHILA
	Organism Taxid	:	93929
	Other Details	:	RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE.
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	U A:7 , G A:8 , MG A:103 , MG A:104 , F A:106 , K A:107 , HOH A:203 , HOH A:204 , HOH A:205	BINDING SITE FOR RESIDUE MG A 101
2	AC2	SOFTWARE	A A:40 , HOH A:201 , HOH A:209 , HOH A:210 , HOH A:211	BINDING SITE FOR RESIDUE MG A 102
3	AC3	SOFTWARE	A A:6 , U A:7 , U A:41 , G A:42 , MG A:101 , MG A:104 , F A:106 , HOH A:202	BINDING SITE FOR RESIDUE MG A 103
4	AC4	SOFTWARE	A A:6 , U A:7 , G A:42 , MG A:101 , MG A:103 , F A:106 , K A:107 , HOH A:204 , HOH A:207 , HOH A:208	BINDING SITE FOR RESIDUE MG A 104
5	AC5	SOFTWARE	G A:52	BINDING SITE FOR RESIDUE MG A 105
6	AC6	SOFTWARE	A A:6 , U A:7 , U A:41 , G A:42 , MG A:101 , MG A:103 , MG A:104 , HOH A:203 , HOH A:204 , HOH A:205 , HOH A:208	BINDING SITE FOR RESIDUE F A 106
7	AC7	SOFTWARE	G A:5 , A A:6 , U A:7 , MG A:101 , MG A:104 , HOH A:204 , HOH A:206	BINDING SITE FOR RESIDUE K A 107

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:RNA  Length:52
                                                                                   
                  4enc A  1 GGGCGAUGAGGCCCGCCCAAACUGCCCUGAAAAGGGCUGAUGGCCUCUACUG 52
                                    10        20        30        40        50

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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
		F	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4enc)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - 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
	4enc
		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 \| HSSP
		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
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

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
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

Description