1N6Z - JenaLib

Title :   SOLUTION NMR STRUCTURE OF PROTEIN YML108W FROM SACCHAROMYCES CEREVISIAE. A NOVEL MEMBER OF THE SPLIT BAB FOLD. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET YT601.

Authors :   A. Pineda-Lucena, C. H. Arrowsmith, Northeast Structural Genomics Consortium (Nesg)

Date :   12 Nov 02 (Deposition) - 06 May 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (10x)

Keywords :   Structural Proteomics, Structural Genomics, Ocsp, Nesg, Protein Structure Initiative, Psi, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Pineda-Lucena, J. C. C. Liao, J. R. Cort, A. Yee, M. A. Kennedy, A. M. Edwards, C. H. Arrowsmith
A Novel Member Of The Split Beta-Alpha-Beta Fold: Solution Structure Of The Hypothetical Protein Yml108W From Saccharomyces Cerevisiae. Ontario Centre For Structural Proteomics Target (Yst0204_1_105); Northeast Structural Genomics Target (Yt601).
Protein Sci. V. 12 1136 2003
PubMed-ID: 12717036 | Reference-DOI: 10.1110/PS.0240903
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 1)

Sequences/Alignments

NMR Structure

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:105
 aligned with YMK8_YEAST | Q03759 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           YMK8_YEAST     1 MSKSNTYRMLVLLEDDTKINKEDEKFLKGKPGKMHEFVDELILPFNVDELDELNTWFDKFDAEICIPNEGHIKYEISSDGLIVLMLDKEIEEVVEKVKKFVEENN 105
               SCOP domains d1n6za_ A: Hypothetical protein Yml108w                                                                   SCOP domains
               CATH domains 1n6zA00 A:1-105  [code=3.10.20.250, no name defined]                                                      CATH domains
               Pfam domains DUF1892-1n6zA01 A:1-105                                                                                   Pfam domains
         Sec.struct. author ......eeeeeee.......................eeeeeee.....hhhhhhhhhhhhhhhhhh.....eeeeee...eeeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-105 UniProt: 1-105                                                                     Transcript 1
                 1n6z A   1 MSKSNTYRMLVLLEDDTKINKEDEKFLKGKPGKMHEFVDELILPFNVDELDELNTWFDKFDAEICIPNEGHIKYEISSDGLIVLMLDKEIEEVVEKVKKFVEENN 105
                                    10        20        30        40        50        60        70        80        90       100

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)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (2, 2)

NMR Structure(hide GO term definitions)

Chain A (YMK8_YEAST | Q03759)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

Visualization

Interactive Views

NMR Structure
	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
(no "Ligands, Modified Residues, Ions" information available for 1n6z)

	Sites
(no "Sites" information available for 1n6z)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1n6z)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models 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
	1n6z
		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
	YMK8_YEAST \| Q03759
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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
	YMK8_YEAST \| Q03759
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description