3NPQ - JenaLib

Title :   STRUCTURE OF THE S-ADENOSYLHOMOCYSTEINE RIBOSWITCH AT 2.18 A

Authors :   F. E. Reyes, A. E. Edwards, R. T. Batey

Date :   28 Jun 10 (Deposition) - 06 Oct 10 (Release) - 03 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.18

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Rna, Riboswitch, S-Adenosyl-Homocysteine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. L. Edwards, F. E. Reyes, A. Heroux, R. T. Batey
Structural Basis For Recognition Of S-Adenosylhomocysteine By Riboswitches.
Rna V. 16 2144 2010
PubMed-ID: 20864509 | Reference-DOI: 10.1261/RNA.2341610

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 18)

Asymmetric Unit (2, 18)

No.	Name	Count	Type	Full Name
1	NCO	15	Ligand/Ion	COBALT HEXAMMINE(III)
2	SAH	3	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	NCO	5	Ligand/Ion	COBALT HEXAMMINE(III)
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	NCO	5	Ligand/Ion	COBALT HEXAMMINE(III)
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	NCO	5	Ligand/Ion	COBALT HEXAMMINE(III)
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Sites (18, 18)

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	G A:15 , C A:16 , A A:29 , G A:30 , G A:31 , C A:32 , G A:47 , HOH A:90 , HOH A:121 , HOH A:250 , HOH A:437 , HOH A:560	BINDING SITE FOR RESIDUE SAH A 55
02	AC2	SOFTWARE	C A:13 , G A:15 , C A:28 , A A:29 , HOH A:326	BINDING SITE FOR RESIDUE NCO A 56
03	AC3	SOFTWARE	A A:24 , G A:25 , HOH A:84 , HOH A:254 , HOH A:320	BINDING SITE FOR RESIDUE NCO A 57
04	AC4	SOFTWARE	G A:15 , C A:16 , A A:17 , A A:18 , G A:19 , C A:26 , C A:27 , C A:28 , HOH A:84 , HOH A:141	BINDING SITE FOR RESIDUE NCO A 58
05	AC5	SOFTWARE	G A:21 , G A:23 , HOH A:491	BINDING SITE FOR RESIDUE NCO A 59
06	AC6	SOFTWARE	G A:7 , A A:9 , HOH A:191 , HOH A:296 , HOH A:348 , HOH A:398 , HOH A:527 , HOH A:531	BINDING SITE FOR RESIDUE NCO A 60
07	AC7	SOFTWARE	U B:14 , G B:15 , C B:16 , A B:29 , G B:30 , G B:31 , C B:32 , G B:47 , HOH B:204	BINDING SITE FOR RESIDUE SAH B 55
08	AC8	SOFTWARE	A B:24 , G B:25 , NCO B:57 , HOH B:168	BINDING SITE FOR RESIDUE NCO B 56
09	AC9	SOFTWARE	G B:15 , C B:16 , A B:17 , A B:18 , G B:19 , C B:26 , C B:27 , C B:28 , NCO B:56 , HOH B:168 , HOH B:359 , HOH B:533	BINDING SITE FOR RESIDUE NCO B 57
10	BC1	SOFTWARE	C B:13 , G B:15 , C B:28 , HOH B:349	BINDING SITE FOR RESIDUE NCO B 58
11	BC2	SOFTWARE	G B:21 , G B:23 , HOH B:75 , HOH B:291	BINDING SITE FOR RESIDUE NCO B 59
12	BC3	SOFTWARE	G B:7 , A B:9 , G B:30 , HOH B:444 , HOH B:452 , HOH B:488 , HOH B:517 , HOH B:530	BINDING SITE FOR RESIDUE NCO B 60
13	BC4	SOFTWARE	G C:15 , C C:16 , A C:29 , G C:30 , G C:31 , C C:32 , G C:47 , HOH C:127 , HOH C:252 , HOH C:460 , HOH C:499	BINDING SITE FOR RESIDUE SAH C 55
14	BC5	SOFTWARE	A C:24 , G C:25 , NCO C:58 , HOH C:139 , HOH C:171 , HOH C:469 , HOH C:532	BINDING SITE FOR RESIDUE NCO C 56
15	BC6	SOFTWARE	C C:13 , G C:15 , C C:28 , HOH C:111 , HOH C:528	BINDING SITE FOR RESIDUE NCO C 57
16	BC7	SOFTWARE	G C:15 , C C:16 , A C:17 , A C:18 , G C:19 , C C:26 , C C:27 , C C:28 , NCO C:56 , HOH C:73	BINDING SITE FOR RESIDUE NCO C 58
17	BC8	SOFTWARE	G C:21 , G C:23 , HOH C:84 , HOH C:381 , HOH C:420	BINDING SITE FOR RESIDUE NCO C 59
18	BC9	SOFTWARE	A C:6 , G C:7 , A C:9 , HOH C:144 , HOH C:314 , HOH C:479	BINDING SITE FOR RESIDUE NCO C 60

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 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:51
                                                                                  
                  3npq A  1 GGACGAGGAGCGCUGCAAGCGAGAGCCCAGGCUCGUCCGAAACGGCGCUCA 54
                                    10        20        30        43        53 
                                                                 39|           
                                                                  43

Chain B from PDB  Type:RNA  Length:49
                                                                                
                  3npq B  1 GGACGAGGAGCGCUGCAAGCGAGAGCCCAGGCUCGUCCAACGGCGCUCA 54
                                    10        20        30       |45         
                                                                38|          
                                                                 44

Chain C from PDB  Type:RNA  Length:50
                                                                                 
                  3npq C  1 GGACGAGGAGCGCUGCAAGCGAGAGCCCAGGCUCGUCCAAACGGCGCUCA 54
                                    10        20        30       |44        54
                                                                38|           
                                                                 43

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 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 ]
		SAH	[ 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 ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3npq)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 \| Biol. Unit 3 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
	3npq
		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