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(-) Description

Title :  UBIQUITIN-CONJUGATING ENZYME E2S
 
Authors :  J. R. Walker, G. V. Avvakumov, S. Xue, E. M. Newman, F. Mackenzie, M. Sund C. Arrowsmith, A. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Consortium (Sgc)
Date :  14 Apr 05  (Deposition) - 03 May 05  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Structural Genomics Consortium, Ubiquitin, Ubiquitin-Conjugating Enzyme, Ligase, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Sheng, J. H. Hong, R. Doherty, T. Srikumar, J. Shloush, G. V. Avvakumov, J. R. Walker, S. Xue, D. Neculai, J. W. Wan, S. K. Kim, C. H. Arrowsmith, B. Raught, S. Dhe-Paganon
A Human Ubiquitin Conjugating Enzyme (E2)-Hect E3 Ligase Structure-Function Screen.
Mol Cell Proteomics V. 11 329 2012
PubMed-ID: 22496338  |  Reference-DOI: 10.1074/MCP.O111.013706

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2S
    ChainsA, B
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28-LIC
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN, RESIDUES 1-156
    GeneUBE2S, E2EPF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-CONJUGATING ENZYME E2-24 KDA, UBIQUITIN-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN, E2-EPF5, OK/SW-CL.73

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:122 , PRO A:123 , ASN A:124 , HOH A:161 , PRO B:123 , ASN B:124BINDING SITE FOR RESIDUE NA A 157
2AC2SOFTWAREASN B:36 , ASP B:39 , ASP B:42 , HOH B:167 , HOH B:192BINDING SITE FOR RESIDUE NA B 157

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:118 -B:118

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:70 -Pro A:71
2Phe B:70 -Pro B:71

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2S_HUMAN14-146
 
  2A:14-146
B:14-146
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2S_HUMAN84-99
 
  2A:84-99
B:84-99
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2S_HUMAN14-146
 
  1A:14-146
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2S_HUMAN84-99
 
  1A:84-99
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2S_HUMAN14-146
 
  1-
B:14-146
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2S_HUMAN84-99
 
  1-
B:84-99
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2S_HUMAN14-146
 
  2A:14-146
B:14-146
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2S_HUMAN84-99
 
  2A:84-99
B:84-99

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002645521ENSE00001303505chr19:55919325-55918955371UBE2S_HUMAN1-110--
1.2ENST000002645522ENSE00000953875chr19:55918330-55918183148UBE2S_HUMAN2-51502A:6-51
B:10-51
46
42
1.3ENST000002645523ENSE00000699548chr19:55915846-55915656191UBE2S_HUMAN51-114642A:51-114
B:51-114
64
64
1.4ENST000002645524ENSE00001187103chr19:55913130-55912652479UBE2S_HUMAN115-2221082A:115-156
B:115-156
42
42

(-) 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:PROTEIN  Length:151
 aligned with UBE2S_HUMAN | Q16763 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:151
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155 
          UBE2S_HUMAN     6 ENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDFPASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRHVLLTIKCLLIHPNPESALNEEAGRLLLENYEEYAARARLLTEIHG 156
               SCOP domains d1zdna1 A:6-156 Ubiquitin conjugating enzyme, UBC                                                                                                       SCOP domains
               CATH domains 1zdnA00 A:6-156 Ubiquitin Conjugating Enzyme                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee...............hhhhhh.......hhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------UBIQUITIN_CONJUGAT_2  PDB: A:14-146 UniProt: 14-146                                                                                  ---------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------UBIQUITIN_CONJUG--------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:6-51 UniProt: 2-51           ---------------------------------------------------------------Exon 1.4  PDB: A:115-156 UniProt: 115-222  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:51-114 UniProt: 51-114                         ------------------------------------------ Transcript 1 (2)
                 1zdn A   6 ENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDFPASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRHVLLTIKCLLIHPNPESALNEEAGRLLLENYEEYAARARLLTEIHG 156
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155 

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with UBE2S_HUMAN | Q16763 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:147
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       
          UBE2S_HUMAN    10 PHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDFPASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRHVLLTIKCLLIHPNPESALNEEAGRLLLENYEEYAARARLLTEIHG 156
               SCOP domains d1zdnb_ B: automated matches                                                                                                                        SCOP domains
               CATH domains 1zdnB00 B:10-156 Ubiquitin Conjugating Enzyme                                                                                                       CATH domains
           Pfam domains (1) -----UQ_con-1zdnB01 B:15-152                                                                                                                   ---- Pfam domains (1)
           Pfam domains (2) -----UQ_con-1zdnB02 B:15-152                                                                                                                   ---- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeee.......eeeeeee..........eeeeeee..........eeee...............hhhhhhh......hhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: B:14-146 UniProt: 14-146                                                                                  ---------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------UBIQUITIN_CONJUG--------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:10-51 UniProt: 2-51      ---------------------------------------------------------------Exon 1.4  PDB: B:115-156 UniProt: 115-222  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3  PDB: B:51-114 UniProt: 51-114                         ------------------------------------------ Transcript 1 (2)
                 1zdn B  10 PHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDFPASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRHVLLTIKCLLIHPNPESALNEEAGRLLLENYEEYAARARLLTEIHG 156
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: UBC (69)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UBE2S_HUMAN | Q16763)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0061631    ubiquitin conjugating enzyme activity    Isoenergetic transfer of ubiquitin from one protein to another via the reaction X-ubiquitin + Y -> Y-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0031145    anaphase-promoting complex-dependent catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0010458    exit from mitosis    The cell cycle transition where a cell leaves M phase and enters a new G1 phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
    GO:0010994    free ubiquitin chain polymerization    The process of creating free ubiquitin chains, compounds composed of a large number of ubiquitin monomers. These chains are not conjugated to a protein.
    GO:1904668    positive regulation of ubiquitin protein ligase activity    Any process that activates or increases the frequency, rate or extent of ubiquitin protein ligase activity.
    GO:0070979    protein K11-linked ubiquitination    A protein ubiquitination process in which ubiquitin monomers are attached to a protein, and then ubiquitin polymers are formed by linkages between lysine residues at position 11 of the ubiquitin monomers. K11-linked polyubiquitination targets the substrate protein for degradation. The anaphase-promoting complex promotes the degradation of mitotic regulators by assembling K11-linked polyubiquitin chains.
    GO:0044314    protein K27-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 27 of the ubiquitin monomers, is added to a protein.
    GO:0035519    protein K29-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 29 of the ubiquitin monomers, is added to a protein. K29-linked ubiquitination targets the substrate protein for degradation.
    GO:0085020    protein K6-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 6 of the ubiquitin monomers, is added to a protein. K6-linked ubiquitination is involved in DNA repair.
    GO:0070534    protein K63-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0005680    anaphase-promoting complex    A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

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        UBE2S_HUMAN | Q167635bnb 5l9t

(-) Related Entries Specified in the PDB File

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