Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF S. POMBE UBA1 IN A CLOSED CONFORMATION
 
Authors :  Z. Lv, L. Yuan, G. Aldana-Masangkay, J. H. Atkison, Y. Chen, S. K. Olsen
Date :  26 Jan 17  (Deposition) - 14 Jun 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann-Like Fold, Ubiquitin-Like Fold, Ubiquitin Activating Enzyme, Atp Binding, Ligase Activity, Atp/Mg Binding, Ubiquitin E2 Binding, Ligase, Transferase, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Lv, L. Yuan, J. H. Atkison, G. Aldana-Masangkay, Y. Chen, S. K. Olsen
Domain Alternation And Active Site Remodeling Are Conserved Structural Features Of Ubiquitin E1.
J. Biol. Chem. 2017
PubMed-ID: 28572513  |  Reference-DOI: 10.1074/JBC.M117.787622

(-) Compounds

Molecule 1 - UBIQUITIN-ACTIVATING ENZYME E1 1
    Chains: A
    EC Number: 6.2.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSMT3
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 562
    Gene: PTR3, SPBC1604.21C, SPBC211.09
    Mutation: YES
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC 24843)
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
    Synonym: POLY(A)+ RNA TRANSPORT PROTEIN 3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
18E71Ligand/Ion2-(DECYLAMINO)ETHANE-1-THIOL
28EA1Ligand/IonN-(2-{[(4-CHLOROPHENYL)METHYL]DISULFANYL}ETHYL)DECAN-1-AMINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:436 , ALA A:437binding site for residue SO4 A 1101
2AC2SOFTWARETYR A:67 , LEU A:115 , GLU A:130 , LYS A:135 , GLU A:138 , GLY A:307binding site for residue 8EA A 1102
3AC3SOFTWAREMET A:944 , CYS A:994binding site for residue 8E7 A 1103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UM6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1His A:202 -Gly A:203
2Lys A:381 -Gln A:382
3Gly A:519 -Ile A:520

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UM6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UM6)

(-) Exons   (0, 0)

(no "Exon" information available for 5UM6)

(-) 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:PROTEIN  Length:962
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee......hhhhhh....hhhhh..hhhhhhhhhhhh......eee.....hhhhhhh.eeee...hhhhhhhhhhhhhhh..eeeeeeee..eeeeeee....eee.........eeeeeeee...eeee............eeeee....hhhhhh...ee.......eee.........eee..eeeee...eee...hhhhhh........hhhhh.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhh.................hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh.......eeeee........hhhhh...hhhhh..hhhhhhhhhhhhhhhhhh..eeee............hhhhhhhh.eeee...hhhhhhhhhhhhhhhh..eeeeeee..eeeeeee...................hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.................hhhhhhhh...hhhhhh................hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhh.eeeee....eeeee......eeee..eeee.....eeee..hhhhhhhhhhhh...eeeeeee..eeeee...hhhhhh.....hhhhhhhhhh.........eeeeeeeee.....ee....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5um6 A   37 QSNVLIIGCKGLGVEIAKNVCLAGVKSVTLYDPQPTRIEDLSSQYFLTEDDIGVPRAKVTVSKLAELNQYVPVSVVDELSTEYLKNFKCVVVTETSLTKQLEINDFTHKNHIAYIAADSRGLFGSIFCDFGENFICTDTDGNEPLTGMIASITDDGVVTMLEETRHGLENGDFVKFTEVKGMPGLNDGTPRKVEVKGPYTFSIGSVKDLGSAGYNGVFTQVKVPTKISFKSLRESLKDPEYVYPDFGKMMRPPQYHIAFQALSAFADAHEGSLPRPRNDIDAAEFFEFCKKIASTLQFDVELDEKLIKEISYQARGDLVAMSAFLGGAVAQEVLKATTSKFYPLKQYFYFDSLESLPSSVTISEETCKPRGCRYDGQIAVFGSEFQEKIASLSTFLVGAGAIGCEMLKNWAMMGVATGESGHISVTDMDSIEKSNLNRQFLFRPRDVGKLKSECASTAVSIMNPSLTGKITSYQERVGPESEGIFGDEFFEKLSLVTNALDNVEARMYVDRRCVFFEKPLLESGTLGTKGNTQVVVPHLTESYGSSQDPPEKSFPIATLKNFPNRIEHTIAWARDLFEGLFKQPIDNVNMYLSSPNFLETSLKTSSNPREVLENIRDYLVTEKPLSFEECIMWARLQFDKFFNNNIQQLLFNFPKDSVTSTGQPFWSGPKRAPTPLSFDIHNREHFDFIVAAASLYAFNYGLKSETDPAIYERVLAGYNPPPFAPKSGIKIQVKQELKSIADSLPPPSSLVGFRLTPAEFEKDDDSNHHIDFITAASNLRAMNYDITPADRFKTKFVAGKIVPAMCTSTAVVSGLVCLELVKLVDGKKKIEEYKNGFFNLAIGLFTFSDPIASPKMKVNGKEIDKIWDRYNLPDCTLQELIDYFQKEEGLEVTMLSSGVSLLYANFQPPKKLAERLPLKISELVEQITKKKLEPFRKHLVLEICCDDANGEDVEVPFICIKL 1012
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766  ||   790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      769|                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       784
   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)

(no "SCOP Domain" information available for 5UM6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UM6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UM6)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    8E7  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    8EA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:519 - Ile A:520   [ RasMol ]  
    His A:202 - Gly A:203   [ RasMol ]  
    Lys A:381 - Gln A:382   [ RasMol ]  
 

(-) 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
  5um6
    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
  UBA1_SCHPO | O94609
    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)
  6.2.1.45
    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
  UBA1_SCHPO | O94609
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UBA1_SCHPO | O94609: 4ii2 4ii3 5knl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5UM6)