1EGK | UH0002 - JenaLib

Title :   CRYSTAL STRUCTURE OF A NUCLEIC ACID FOUR-WAY JUNCTION

Authors :   J. Nowakowski, P. J. Shim, C. D. Stout, G. F. Joyce

Date :   15 Feb 00 (Deposition) - 26 Jun 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Four-Way Junction, Nucleic Acid, Rna-Dna Complex, 10-23 Dna Enzyme, Ribozyme, Dna/Rna Complex, Dna-Rna Hybrid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Nowakowski, P. J. Shim, C. D. Stout, G. F. Joyce
Alternative Conformations Of A Nucleic Acid Four-Way Junction.
J. Mol. Biol. V. 300 93 2000
PubMed-ID: 10864501 | Reference-DOI: 10.1006/JMBI.2000.3826
(for further references see the PDB file header)

Compounds

*Molecule 1 - RNA (5'- R(APGPGPAPGPAPGPAPGPAPUPGPGPGPUPGPCPGPAP G)-3')*
	Chains	:	A, C
	Engineered	:	YES
	Other Details	:	RNA SUBSTRATE
	Other Details - Source	:	DNA AND RNA WERE SYNTHESIZED ON SOLID SUPPORT USING PHOSPHORAMIDITE CHEMISTRY
	Synthetic	:	YES

Molecule 2 - 10-23 DNA ENZYME
	Chains	:	B, D
	Engineered	:	YES
	Other Details	:	10-23 DNA ENZYME BOUND TO RNA SUBSTRATE
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 14)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:28 , HOH A:29 , HOH A:30 , HOH A:31 , HOH A:32 , HOH A:33	BINDING SITE FOR RESIDUE MG A 21
02	AC2	SOFTWARE	HOH B:55 , HOH B:56 , HOH B:57 , HOH B:58 , HOH B:59 , HOH B:60	BINDING SITE FOR RESIDUE MG A 22
03	AC3	SOFTWARE	HOH B:61 , HOH C:28 , HOH C:29 , HOH C:30 , HOH C:31 , HOH C:32	BINDING SITE FOR RESIDUE MG C 3
04	AC4	SOFTWARE	HOH B:62 , HOH B:63 , HOH C:34 , HOH C:35 , HOH C:36 , HOH C:37	BINDING SITE FOR RESIDUE MG C 4
05	AC5	SOFTWARE	HOH A:34 , HOH A:35 , HOH A:36 , HOH A:37 , HOH A:38 , HOH A:39	BINDING SITE FOR RESIDUE MG A 23
06	AC6	SOFTWARE	HOH C:45 , HOH C:46 , HOH C:47 , HOH C:48 , HOH C:49 , HOH C:50 , G C:113	BINDING SITE FOR RESIDUE MG C 6
07	AC7	SOFTWARE	HOH C:51 , HOH C:53 , HOH C:56 , HOH D:52 , HOH D:54 , HOH D:55	BINDING SITE FOR RESIDUE MG C 7
08	AC8	SOFTWARE	HOH A:40 , HOH A:41 , HOH A:42 , HOH A:43 , HOH A:44 , HOH A:45	BINDING SITE FOR RESIDUE MG A 24
09	AC9	SOFTWARE	HOH B:64 , HOH C:64 , HOH C:65 , HOH C:67 , HOH C:68 , G C:103 , HOH D:63	BINDING SITE FOR RESIDUE MG C 9
10	BC1	SOFTWARE	G A:3 , HOH A:46 , HOH A:47 , HOH A:48 , HOH B:65 , HOH B:66 , HOH D:70	BINDING SITE FOR RESIDUE MG A 25
11	BC2	SOFTWARE	G A:16 , HOH A:49 , HOH A:50 , HOH A:51 , HOH A:52 , HOH A:53 , HOH A:54	BINDING SITE FOR RESIDUE MG A 26
12	BC3	SOFTWARE	HOH A:55 , HOH A:56 , HOH A:57 , HOH A:58 , HOH A:59 , HOH A:60	BINDING SITE FOR RESIDUE MG A 27
13	BC4	SOFTWARE	HOH C:87 , HOH C:88 , HOH C:90 , HOH C:91 , HOH C:92 , U C:115 , HOH D:89	BINDING SITE FOR RESIDUE MG C 13
14	BC5	SOFTWARE	HOH C:93 , HOH C:94 , HOH C:95 , HOH C:96 , HOH C:97 , HOH C:98	BINDING SITE FOR RESIDUE MG C 14

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:DNA/RNA  Length:20
                                                    
                 1egk A   1 AGGAGAGAGAUGGGUGCGAG  20
                                    10        20

Chain B from PDB  Type:DNA  Length:34
                                                                  
                 1egk B  21 CTCGCACCCAGGCTAGCTACAACGACTCTCTCCT  54
                                    30        40        50

Chain C from PDB  Type:DNA/RNA  Length:20
                                                    
                 1egk C 101 AGGAGAGAGAUGGGUGCGAG 120
                                   110       120

Chain D from PDB  Type:DNA  Length:34
                                                                  
                 1egk D 121 CTCGCACCCAGGCTAGCTACAACGACTCTCTCCT 154
                                   130       140       150

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
		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 ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1egk)

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
	1egk
		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