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Description

Title :   X-RAY STRUCTURE OF YBL001C NORTHEAST STRUCTURAL GENOMICS (NESG) CONSORTIUM TARGET YTYST72

Authors :   X. Tao, R. Khayat, D. Christendat, A. Savchenko, X. Xu, A. Edwards, C. H. Arrowsmith, L. Tong, Northeast Structural Genomics Consort (Nesg)

Date :   05 Jun 02 (Deposition) - 29 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Hypothetical Protein, Htb2-Nth2 Intergenic Region, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Tao, R. Khayat, D. Christendat, A. Savchenko, X. Xu, S. Goldsmith-Fischman, B. Honig, A. Edwards, C. H. Arrowsmith, L. Ton
Crystal Structures Of Mth1187 And Its Yeast Ortholog Ybl001
Proteins V. 52 478 2003
PubMed-ID: 12866058 | Reference-DOI: 10.1002/PROT.10443

Compounds

Molecule 1 - HYPOTHETICAL 11.5KDA PROTEIN IN HTB2-NTH2 INTERGENIC REGION
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	YBL001C

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 4)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:21 , ILE A:22 , SER A:23 , ARG A:74 , ARG A:84 , LYS A:87 , GLN A:89 , HOH A:261 , HOH A:427	BINDING SITE FOR RESIDUE SO4 A 224

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1LXJ)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 1LXJ)

Exons (1, 1)

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YBL001C	1	YBL001C.1	II:237469-237155	315	ECM15_YEAST	1-104	104	1	A:1-104	104

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
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Chain A from PDB  Type:PROTEIN  Length:104
 aligned with ECM15_YEAST | P35195 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:104
                                    10        20        30        40        50        60        70        80        90       100    
          ECM15_YEAST     1 MPKIFCLADVCMVPIGTDSASISDFVALIEKKIRESPLKSTLHSAGTTIEGPWDDVMGLIGEIHEYGHEKGYVRVHTDIRVGTRTDKHQTAQDKIDVVLKKISQ 104
               SCOP domains d1lxja_ A: Hypothetical protein YB1001C                                                                  SCOP domains
               CATH domains -1lxjA00 A:2-104  [code=3.30.70.930, no name defined]                                                    CATH domains
               Pfam domains -------DUF77-1lxjA01 A:8-99                                                                        ----- Pfam domains
         Sec.struct. author ....eeeeeeeeeee......hhhhhhhhhhhhhh...eeeee..eeeeeeehhhhhhhhhhhhhhhhhh...eeeeeeeee.......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-104 UniProt: 1-104                                                                    Transcript 1
                 1lxj A   1 mPKIFCLADVCmVPIGTDSASISDFVALIEKKIRESPLKSTLHSAGTTIEGPWDDVmGLIGEIHEYGHEKGYVRVHTDIRVGTRTDKHQTAQDKIDVVLKKISQ 104
                            |       10 |      20        30        40        50      | 60        70        80        90       100    
                            |         12-MSE                                       57-MSE                                           
                            1-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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: MTH1187/YkoF-like (11)

Family: MTH1187-like (5)

Protein domain: Hypothetical protein YB1001C (1)

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

d1lxja_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.930, no name defined] (10)

Baker's yeast (Saccharomyces cerevisiae) (1)

1lxjA00

A:2-104

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MTH1187-YkoF (6)

Family: DUF77 (4)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (1)

DUF77-1lxjA01

A:8-99

Gene Ontology (4, 4)

Asymmetric Unit(hide GO term definitions)

Chain A (ECM15_YEAST | P35195)

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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (1, 1)

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Related Entries

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