5DEK - JenaLib

Asymmetric Unit

Asym. Unit - sites

Biological Unit 1

Biol. Unit 1 - sites

Biological Unit 2

collapse

expand

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Description

Title :   RNA OCTAMER CONTAINING DT

Authors :   J. M. Harp, M. Egli

Date :   25 Aug 15 (Deposition) - 20 Jul 16 (Release) - 20 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.99

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

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

Reference :   A. V. Kel In, I. Zlatev, J. Harp, M. Jayaraman, A. Bisbe, J. O Shea, N. Taneja, R. M. Manoharan, S. Khan, K. Charisse, M. A. Maier, M. Egli, K. G. Rajeev, M. Manoharan
Structural Basis Of Duplex Thermodynamic Stability And Enhanced Nuclease Resistance Of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides.
J. Org. Chem. V. 81 2261 2016
PubMed-ID: 26940174 | Reference-DOI: 10.1021/ACS.JOC.5B02375

Compounds

Molecule 1 - RNA OLIGONUCLEOTIDE CONTAINING DT
	Chains	:	A, B, C, D
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Structural Features

Chains, Units

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NCO	2	Ligand/Ion	COBALT HEXAMMINE(III)

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NCO	1	Ligand/Ion	COBALT HEXAMMINE(III)

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NCO	1	Ligand/Ion	COBALT HEXAMMINE(III)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	C A:107 , G A:108 , A B:212 , HOH B:405 , U C:106 , C C:107	binding site for residue NCO B 301
2	AC2	SOFTWARE	U A:106 , C A:107 , A C:103 , A C:104 , G C:108 , HOH C:301	binding site for residue NCO C 201

SS Bonds (0, 0)

(no "SS Bond" information available for 5DEK)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 5DEK)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 5DEK)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 5DEK)

Exons (0, 0)

(no "Exon" information available for 5DEK)

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:DNA/RNA  Length:8
                                        
                 5dek A 101 CGAATUCG 108

Chain B from PDB  Type:DNA/RNA  Length:8
                                        
                 5dek B 209 CGAATUCG 216

Chain C from PDB  Type:DNA/RNA  Length:8
                                        
                 5dek C 101 CGAATUCG 108

Chain D from PDB  Type:DNA/RNA  Length:8
                                        
                 5dek D 209 CGAATUCG 216

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)

(no "SCOP Domain" information available for 5DEK)

CATH Domains (0, 0)

(no "CATH Domain" information available for 5DEK)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 5DEK)

Gene Ontology (0, 0)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 5DEK)

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

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dek)

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 \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites 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
	5dek
		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