Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  HUMAN UBIQUITIN CONJUGATING ENZYME E2E2
 
Authors :  J. R. Walker, G. V. Avvakumov, E. M. Newman, F. Mackenzie, I. Kozieradzk A. Bochkarev, M. Sundstrom, C. Arrowsmith, A. Edwards, S. Dhe-Pagano Structural Genomics Consortium (Sgc)
Date :  06 Dec 04  (Deposition) - 11 Jan 05  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (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 E2E2
    ChainsA, B, C
    EC Number6.3.2.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 55-201
    GeneUBE2E2, UBCH8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUBIQUITIN-PROTEIN LIGASE E2, UBIQUITIN CARRIER PROTEIN E2, UBCH8

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Y6L)

(-) Sites  (0, 0)

(no "Site" information available for 1Y6L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y6L)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:60 -Pro A:61
2Tyr B:60 -Pro B:61
3Tyr C:60 -Pro C:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y6L)

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2E2_HUMAN58-190
 
 
  3A:4-136
B:4-136
C:4-136
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2E2_HUMAN128-143
 
 
  3A:74-89
B:74-89
C:74-89
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2E2_HUMAN58-190
 
 
  1A:4-136
-
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2E2_HUMAN128-143
 
 
  1A:74-89
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2E2_HUMAN58-190
 
 
  1-
B:4-136
-
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2E2_HUMAN128-143
 
 
  1-
B:74-89
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2E2_HUMAN58-190
 
 
  1-
-
C:4-136
2UBIQUITIN_CONJUGAT_1PS00183 Ubiquitin-conjugating enzymes active site.UB2E2_HUMAN128-143
 
 
  1-
-
C:74-89

(-) Exons   (5, 15)

Asymmetric Unit (5, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003967032aENSE00001525976chr3:23244784-23244955172UB2E2_HUMAN-00--
1.3aENST000003967033aENSE00001525974chr3:23250183-23250366184UB2E2_HUMAN1-59593A:0-5
B:0-5
C:0-5
6
6
6
1.4ENST000003967034ENSE00001648562chr3:23258753-2325880351UB2E2_HUMAN59-76183A:5-22
B:5-22
C:5-22
18
18
18
1.7ENST000003967037ENSE00001730682chr3:23541099-23541231133UB2E2_HUMAN76-120453A:22-66
B:22-66
C:22-66
45
45
45
1.8bENST000003967038bENSE00001629049chr3:23574045-23574192148UB2E2_HUMAN121-170503A:67-116
B:67-116
C:67-116
50
50
50
1.9dENST000003967039dENSE00001525971chr3:23631225-236332842060UB2E2_HUMAN170-201323A:116-147
B:116-147
C:116-147
32
32
32

(-) 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:148
 aligned with UB2E2_HUMAN | Q96LR5 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:148
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193        
          UB2E2_HUMAN    54 STSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT 201
               SCOP domains d1y6la_ A: Ubiquitin conjugating enzyme, UBC                                                                                                         SCOP domains
               CATH domains 1y6lA00 A:0-147 Ubiquitin Conjugating Enzyme                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: A:4-136 UniProt: 58-190                                                                                   ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.3a  ----------------Exon 1.7  PDB: A:22-66 UniProt: 76-120       Exon 1.8b  PDB: A:67-116 UniProt: 121-170         ------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.4          ---------------------------------------------------------------------------------------------Exon 1.9d  PDB: A:116-147        Transcript 1 (2)
                 1y6l A   0 STSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139        

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with UB2E2_HUMAN | Q96LR5 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:148
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193        
          UB2E2_HUMAN    54 STSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT 201
               SCOP domains d1y6lb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                         SCOP domains
               CATH domains 1y6lB00 B:0-147 Ubiquitin Conjugating Enzyme                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: B:4-136 UniProt: 58-190                                                                                   ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.3a  ----------------Exon 1.7  PDB: B:22-66 UniProt: 76-120       Exon 1.8b  PDB: B:67-116 UniProt: 121-170         ------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.4          ---------------------------------------------------------------------------------------------Exon 1.9d  PDB: B:116-147        Transcript 1 (2)
                 1y6l B   0 STSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139        

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with UB2E2_HUMAN | Q96LR5 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:148
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193        
          UB2E2_HUMAN    54 STSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT 201
               SCOP domains d1y6lc_ C: Ubiquitin conjugating enzyme, UBC                                                                                                         SCOP domains
               CATH domains 1y6lC00 C:0-147 Ubiquitin Conjugating Enzyme                                                                                                         CATH domains
           Pfam domains (1) -----UQ_con-1y6lC01 C:5-142                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) -----UQ_con-1y6lC02 C:5-142                                                                                                                    ----- Pfam domains (2)
           Pfam domains (3) -----UQ_con-1y6lC03 C:5-142                                                                                                                    ----- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: C:4-136 UniProt: 58-190                                                                                   ----------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------UBIQUITIN_CONJUG---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.3a  ----------------Exon 1.7  PDB: C:22-66 UniProt: 76-120       Exon 1.8b  PDB: C:67-116 UniProt: 121-170         ------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.4          ---------------------------------------------------------------------------------------------Exon 1.9d  PDB: C:116-147        Transcript 1 (2)
                 1y6l C   0 STSAKRIQKELAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139        

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: UBC (69)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (UB2E2_HUMAN | Q96LR5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042296    ISG15 transferase activity    Catalysis of the transfer of ISG15 from one protein to another via the reaction X-ISG15 + Y --> Y-ISG15 + X, where both X-ISG15 and Y-ISG15 are covalent linkages.
    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: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: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:0032020    ISG15-protein conjugation    The covalent addition to a protein of ISG15, a ubiquitin-like protein.
    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:1900087    positive regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that promotes the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    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:0070936    protein K48-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.
    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.

 Visualization

(-) Interactive Views

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
(no "Ligands, Modified Residues, Ions" information available for 1y6l)
 
  Sites
(no "Sites" information available for 1y6l)
 
  Cis Peptide Bonds
    Tyr A:60 - Pro A:61   [ RasMol ]  
    Tyr B:60 - Pro B:61   [ RasMol ]  
    Tyr C:60 - Pro C:61   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) 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
  1y6l
    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
  UB2E2_HUMAN | Q96LR5
    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
  UB2E2_HUMAN | Q96LR5
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1Y6L)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Y6L)