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

(-) Description

Title :  CRYSTAL STRUCTURE OF HMMS2-HUBC13
 
Authors :  T. F. Moraes, R. A. Edwards, S. Mckenna, L. Pashushok, W. Xiao, J. N. M. Glover, M. J. Ellison
Date :  16 May 01  (Deposition) - 08 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ubiquitin, Ubc, Dna Repair, Traf6, Nfkb, , Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. F. Moraes, R. A. Edwards, S. Mckenna, L. Pastushok, W. Xiao, J. N. Glover, M. J. Ellison
Crystal Structure Of The Human Ubiquitin Conjugating Enzyme Complex, Hmms2-Hubc13.
Nat. Struct. Biol. V. 8 669 2001
PubMed-ID: 11473255  |  Reference-DOI: 10.1038/90373
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MMS2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - UBIQUITIN-CONJUGATING ENZYME E2-17 KDA
    ChainsB
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBC13

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1J7D)

(-) Sites  (0, 0)

(no "Site" information available for 1J7D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J7D)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:73 -Pro A:74
2Tyr B:62 -Pro B:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052431E36GUB2V2_HUMANPolymorphism11557776AE36G
2UniProtVAR_052433P78QUB2V2_HUMANPolymorphism11557786AP78Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UBE2N_HUMAN6-138  1B:6-138
UB2V2_HUMAN13-138  1A:13-138
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UBE2N_HUMAN76-91  1B:76-91

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003180661ENSE00001277525chr12:93836026-93835631396UBE2N_HUMAN1-10101B:2-109
1.3ENST000003180663ENSE00001277541chr12:93805075-93804829247UBE2N_HUMAN11-93831B:11-9383
1.4ENST000003180664ENSE00001277519chr12:93804650-93804510141UBE2N_HUMAN93-140481B:93-14048
1.5ENST000003180665ENSE00001277538chr12:93803855-938020901766UBE2N_HUMAN140-152131B:140-15011

(-) 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:140
 aligned with UB2V2_HUMAN | Q15819 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:140
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145
          UB2V2_HUMAN     6 GVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN 145
               SCOP domains d1j7da_ A: Ubiquitin conjugating enzyme, UBC                                                                                                 SCOP domains
               CATH domains 1j7dA00 A:6-145 Ubiquitin Conjugating Enzyme                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.....eeeee.........eeeeeee..........eeeeeee..........eeee................hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------G-----------------------------------------Q------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------UBIQUITIN_CONJUGAT_2  PDB: A:13-138 UniProt: 13-138                                                                           ------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j7d A   6 GVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN 145
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with UBE2N_HUMAN | P61088 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:149
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         
          UBE2N_HUMAN     2 AGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
               SCOP domains d1j7db_ B: Ubiquitin conjugating enzyme, UBC                                                                                                          SCOP domains
               CATH domains 1j7dB00 B:2-150 Ubiquitin Conjugating Enzyme                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh......eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: B:6-138 UniProt: 6-138                                                                                    ------------ PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------UBIQUITIN_CONJUG----------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1 Exon 1.3  PDB: B:11-93 UniProt: 11-93                                              ----------------------------------------------Exon 1.5    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------Exon 1.4  PDB: B:93-140 UniProt: 93-140         ---------- Transcript 1 (2)
                 1j7d B   2 AGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN 150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141         

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J7D)

(-) Gene Ontology  (50, 67)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UB2V2_HUMAN | Q15819)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
biological process
    GO:0000729    DNA double-strand break processing    The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0042275    error-free postreplication DNA repair    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA via processes such as template switching, which does not remove the replication-blocking lesions but does not increase the endogenous mutation rate.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0045739    positive regulation of DNA repair    Any process that activates or increases the frequency, rate or extent of DNA repair.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0032436    positive regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0051965    positive regulation of synapse assembly    Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0006301    postreplication repair    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
    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:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0006282    regulation of DNA repair    Any process that modulates the frequency, rate or extent of DNA repair.
cellular component
    GO:0031372    UBC13-MMS2 complex    A heterodimeric ubiquitin conjugating enzyme complex that catalyzes assembly of K63-linked polyubiquitin chains, which act as a signal to promote error-free DNA postreplication repair; in Saccharomyces the complex comprises Ubc13p and Mms2p.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

Chain B   (UBE2N_HUMAN | P61088)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    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:0000729    DNA double-strand break processing    The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0016574    histone ubiquitination    The modification of histones by addition of ubiquitin groups.
    GO:0070423    nucleotide-binding oligomerization domain containing signaling pathway    Any series of molecular signals generated as a consequence of binding to a nucleotide-binding oligomerization domain containing (NOD) protein.
    GO:0045739    positive regulation of DNA repair    Any process that activates or increases the frequency, rate or extent of DNA repair.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0031058    positive regulation of histone modification    Any process that activates or increases the frequency, rate or extent of the covalent alteration of a histone.
    GO:0051443    positive regulation of ubiquitin-protein transferase activity    Any process that activates, maintains or increases the rate of ubiquitin transferase activity.
    GO:0006301    postreplication repair    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
    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.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006282    regulation of DNA repair    Any process that modulates the frequency, rate or extent of DNA repair.
    GO:0033182    regulation of histone ubiquitination    Any process that modulates the frequency, rate or extent of the addition of a ubiquitin group to a histone protein.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    GO:0006511    ubiquitin-dependent protein 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 a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0031372    UBC13-MMS2 complex    A heterodimeric ubiquitin conjugating enzyme complex that catalyzes assembly of K63-linked polyubiquitin chains, which act as a signal to promote error-free DNA postreplication repair; in Saccharomyces the complex comprises Ubc13p and Mms2p.
    GO:0035370    UBC13-UEV1A complex    A heterodimeric ubiquitin conjugating enzyme complex that catalyzes assembly of K63-linked polyubiquitin chains and is involved in NF-kappaB activation. In humans at least, the complex comprises the ubiquitin-conjugating enzyme UBC13 and ubiquitin-conjugating enzyme variant 1A (UEV1A).
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

 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
(no "Ligands, Modified Residues, Ions" information available for 1j7d)
 
  Sites
(no "Sites" information available for 1j7d)
 
  Cis Peptide Bonds
    Tyr A:73 - Pro A:74   [ RasMol ]  
    Tyr B:62 - Pro B:63   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1j7d
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  UB2V2_HUMAN | Q15819
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  UBE2N_HUMAN | P61088
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.3.2.19
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  UB2V2_HUMAN | Q15819
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  UBE2N_HUMAN | P61088
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        UB2V2_HUMAN | Q158191j74 1zgu 3von 4nr3 4nrg 4nri 4onl 4onm 4onn 4orh 5ait
        UBE2N_HUMAN | P610882c2v 3hct 3hcu 3von 3w31 4dhi 4dhj 4dhz 4ip3 4nr3 4nrg 4nri 4onl 4onm 4onn 4orh 4tkp 4whv 5ait 5aiu 5eya

(-) Related Entries Specified in the PDB File

1j74 1J74 IS THE MONOMERIC CRYSTAL STRUCTURE OF MMS2