1JZT - JenaLib

Asym.Unit - manually (Jmol Viewer)

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)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YEAST YNU0, YNL200C

Authors :   J. -S. Jiang, N. O. Manning, S. K. Burley, New York Sgx Research Cent Structural Genomics (Nysgxrc)

Date :   17 Sep 01 (Deposition) - 26 Sep 01 (Release) - 26 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

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

Keywords :   Yeast Hypothetical Protein, Structural Genomics, Selenomethionine, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. -S. Jiang, N. O. Manning, S. Eswaramoorthy, S. E. Gerchman, D. Kumaran, J. H. Kycia, H. A. Lewis, S. Swaminathan, F. W. Studier
Crystal Structure Of Yeast Hypothetical Protein Ynu0_yeast
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL 27.5 KDA PROTEIN IN SPX19-GCR2 INTERGENIC REGION
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 13A
	Expression System Strain	:	B834 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YNL200C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:70 , GLY A:142 , SER A:144	BINDING SITE FOR RESIDUE CL A 401
2	AC2	SOFTWARE	ASN B:70 , GLY B:142	BINDING SITE FOR RESIDUE CL B 402

(no "SS Bond" information available for 1JZT)

Asymmetric Unit

No.	Residues
1	Pro A:147	-	Pro A:148
2	Glu A:151	-	Pro A:152
3	Gln A:187	-	Pro A:188
4	Pro B:147	-	Pro B:148
5	Glu B:151	-	Pro B:152
6	Gln B:187	-	Pro B:188

(no "SAP(SNP)/Variant" information available for 1JZT)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_N	PS51385	YjeF N-terminal domain profile.	NNRE_YEAST	12-234	2	A:12-234 B:12-234

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_N	PS51385	YjeF N-terminal domain profile.	NNRE_YEAST	12-234	1	A:12-234 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_N	PS51385	YjeF N-terminal domain profile.	NNRE_YEAST	12-234	1	- B:12-234

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	YJEF_N	PS51385	YjeF N-terminal domain profile.	NNRE_YEAST	12-234	2	A:12-234 B:12-234

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNL200C	1	YNL200C.1	XIV:264454-263714	741	NNRE_YEAST	1-246	246	2	A:4-246 B:4-246	243 243

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:PROTEIN  Length:243
 aligned with NNRE_YEAST | P40165 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:243
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
           NNRE_YEAST     4 LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGKTETEKGKHVFVIAGPGNNGGDGLVCARHLKLFGYNPVVFYPKRSERTEFYKQLVHQLNFFKVPVLSQDEGNWLEYLKPEKTLCIVDAIFGFSFKPPMREPFKGIVEELCKVQNIIPIVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIRENQTTHYVGGRFIPRDFANKFGFEPFGYESTDQILKL 246
               SCOP domains d1jzta_ A: Hypothetical protein YNL200c (YNU0_YEAST)                                                                                                                                                                                                SCOP domains
               CATH domains 1jztA00 A:4-246 YjeF N-terminal domain-like                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee..hhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh...ee.....hhhhhhh...eeeeeee............hhhhhhhhhhhhh....eeee.....................eeeee...hhhhhhh.....eeeee....hhhhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------YJEF_N  PDB: A:12-234 UniProt: 12-234                                                                                                                                                                                          ------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-246 UniProt: 1-246 [INCOMPLETE]                                                                                                                                                                                                  Transcript 1
                 1jzt A   4 LKVVSSKLAAEIDKELmGPQIGFTLQQLmELAGFSVAQAVCRQFPLRGKTETEKGKHVFVIAGPGNNGGDGLVCARHLKLFGYNPVVFYPKRSERTEFYKQLVHQLNFFKVPVLSQDEGNWLEYLKPEKTLCIVDAIFGFSFKPPmREPFKGIVEELCKVQNIIPIVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIRENQTTHYVGGRFIPRDFANKFGFEPFGYESTDQILKL 246
                                    13      | 23        33        43        53        63        73        83        93       103       113       123       133       143     | 153       163       173       183       193       203       213       223       233       243   
                                           20-MSE      32-MSE                                                                                                              149-MSE

Chain B from PDB  Type:PROTEIN  Length:243
 aligned with NNRE_YEAST | P40165 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:243
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
           NNRE_YEAST     4 LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGKTETEKGKHVFVIAGPGNNGGDGLVCARHLKLFGYNPVVFYPKRSERTEFYKQLVHQLNFFKVPVLSQDEGNWLEYLKPEKTLCIVDAIFGFSFKPPMREPFKGIVEELCKVQNIIPIVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIRENQTTHYVGGRFIPRDFANKFGFEPFGYESTDQILKL 246
               SCOP domains d1jztb_ B: Hypothetical protein YNL200c (YNU0_YEAST)                                                                                                                                                                                                SCOP domains
               CATH domains 1jztB00 B:4-246 YjeF N-terminal domain-like                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee..hhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh...ee.....hhhhhhh...eeeeeee............hhhhhhhhhhhhh....eeee.....................eeeee...hhhhhhh.....eeeee....hhhhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------YJEF_N  PDB: B:12-234 UniProt: 12-234                                                                                                                                                                                          ------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:4-246 UniProt: 1-246 [INCOMPLETE]                                                                                                                                                                                                  Transcript 1
                 1jzt B   4 LKVVSSKLAAEIDKELmGPQIGFTLQQLmELAGFSVAQAVCRQFPLRGKTETEKGKHVFVIAGPGNNGGDGLVCARHLKLFGYNPVVFYPKRSERTEFYKQLVHQLNFFKVPVLSQDEGNWLEYLKPEKTLCIVDAIFGFSFKPPmREPFKGIVEELCKVQNIIPIVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIRENQTTHYVGGRFIPRDFANKFGFEPFGYESTDQILKL 246
                                    13      | 23        33        43        53        63        73        83        93       103       113       123       133       143     | 153       163       173       183       193       203       213       223       233       243   
                                           20-MSE      32-MSE                                                                                                              149-MSE

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: YjeF N-terminal domain-like (30)

Superfamily: YjeF N-terminal domain-like (30)

Family: YjeF N-terminal domain-like (22)

Protein domain: Hypothetical protein YNL200c (YNU0_YEAST) (1)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

1a	d1jzta_	A:
1b	d1jztb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: YjeF N-terminal domain-like (4)

Baker's yeast (Saccharomyces cerevisiae) (1)

1a	1jztA00	A:4-246
1b	1jztB00	B:4-246

(no "Pfam Domain" information available for 1JZT)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NNRE_YEAST | P40165)

molecular function
	GO:0052856	NADHX epimerase activity	Catalysis of the reaction: (R)-NADHX = (S)-NADHX.
	GO:0052857	NADPHX epimerase activity	Catalysis of the reaction: (R)-NADPHX = (S)-NADPHX.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0046496	nicotinamide nucleotide metabolic process	The chemical reactions and pathways involving nicotinamide nucleotides, any nucleotide that contains combined nicotinamide.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Gln A:187 - Pro A:188	[ RasMol ]
		Gln B:187 - Pro B:188	[ RasMol ]
		Glu A:151 - Pro A:152	[ RasMol ]
		Glu B:151 - Pro B:152	[ RasMol ]
		Pro A:147 - Pro A:148	[ RasMol ]
		Pro B:147 - Pro B:148	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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)

Access by PDB/NDB ID
	1jzt
		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
	NNRE_YEAST \| P40165
		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

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
	NNRE_YEAST \| P40165
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1JZT)

(no "Related Entries Specified in the PDB File" available for 1JZT)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File