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

(-) Description

Title :  HHARI/ARIH1-UBCH7~UBIQUITIN
 
Authors :  D. J. Miller, B. A. Schulman
Date :  27 Dec 16  (Deposition) - 14 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.24
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  E2 Ligase, Rbr E3 Ligase, Ubiquitin, Heterotrimer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. K. Dove, J. L. Olszewski, L. Martino, D. M. Duda, X. S. Wu, D. J. Miller K. H. Reiter, K. Rittinger, B. A. Schulman, R. E. Klevit
Structural Studies Of Hhari/Ubch7Ub Reveal Unique E2Ub Conformational Restriction By Rbr Ring1.
Structure V. 25 890 2017
PubMed-ID: 28552575  |  Reference-DOI: 10.1016/J.STR.2017.04.013

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE ARIH1
    ChainsA, B
    EC Number2.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPARG4
    Expression System Taxid1182032
    FragmentUNP RESIDUES 90-557
    GeneARIH1, ARI, MOP6, UBCH7BP, HUSSY-27
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymH7-AP2,HHARI,MONOCYTE PROTEIN 6,MOP-6,PROTEIN ARIADNE-1 HOMOLOG,ARI-1,UBCH7-BINDING PROTEIN,UBCM4-INTERACTING PROTEIN, UBIQUITIN-CONJUGATING ENZYME E2-BINDING PROTEIN 1
 
Molecule 2 - UBIQUITIN-CONJUGATING ENZYME E2 L3
    ChainsC, D
    EC Number2.3.2.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPARG4
    Expression System Taxid1182032
    FragmentUNP RESIDUES 1-154
    GeneUBE2L3, UBCE7, UBCH7
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymE2 UBIQUITIN-CONJUGATING ENZYME L3,L-UBC,UBCH7,UBIQUITIN CARRIER PROTEIN L3,UBIQUITIN-CONJUGATING ENZYME E2-F1,UBIQUITIN- PROTEIN LIGASE L3
 
Molecule 3 - UBIQUITIN C VARIANT
    ChainsE
    EngineeredYES
    Expression SystemESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPARG4
    Expression System Taxid1182032
    FragmentUNP RESIDUES 17-92
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsHEXA-HIS N-TERMINAL TAGGED PROTEIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)A C E
Biological Unit 2 (1x) B D 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1ZN12Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:344 , CYS A:347 , CYS A:362 , CYS A:367binding site for residue ZN A 601
02AC2SOFTWARECYS A:372 , CYS A:375 , HIS A:382 , CYS A:389binding site for residue ZN A 602
03AC3SOFTWARECYS A:276 , CYS A:281 , CYS A:297 , CYS A:299binding site for residue ZN A 603
04AC4SOFTWARECYS A:304 , CYS A:307 , HIS A:312 , CYS A:317binding site for residue ZN A 604
05AC5SOFTWARECYS A:186 , CYS A:189 , CYS A:208 , CYS A:211binding site for residue ZN A 605
06AC6SOFTWARECYS A:203 , HIS A:205 , CYS A:231 , ALA A:233 , CYS A:236binding site for residue ZN A 606
07AC7SOFTWARECYS B:344 , CYS B:347 , CYS B:362 , CYS B:367binding site for residue ZN B 601
08AC8SOFTWARECYS B:372 , CYS B:375 , HIS B:382 , CYS B:389binding site for residue ZN B 602
09AC9SOFTWARECYS B:276 , CYS B:281 , CYS B:297 , CYS B:299binding site for residue ZN B 603
10AD1SOFTWARECYS B:304 , CYS B:307 , HIS B:312 , CYS B:317binding site for residue ZN B 604
11AD2SOFTWARECYS B:186 , CYS B:189 , CYS B:208 , CYS B:211binding site for residue ZN B 605
12AD3SOFTWARECYS B:203 , HIS B:205 , CYS B:231 , CYS B:236binding site for residue ZN B 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Trp A:379 -Glu A:380
2Pro C:44 -Pro C:45
3Tyr C:61 -Pro C:62
4Glu B:222 -Glu B:223
5Trp B:379 -Glu B:380
6Pro D:44 -Pro D:45
7Tyr D:61 -Pro D:62

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UDH)

(-) 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:411
                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhh.............hhh.eee.....eeehhhhhhhhhhhh........ee........eehhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eee.......eeeee......eee.....eee...........hhhhhhhhhhh.....eee......eee......eee........eee.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5udh A  98 DYRYEVLTAEQILQHMVECIREVNEVIQNPATITRILLSHFNWDKEKLMERYFDGNLEKLFAECHAQDMPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILVDDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCGRQFCFNCGENWHDPVKCKWLKKWIKKCDDANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYALQRYLFYCNRYMNHMQSLRFEHKLYAQVKQKMEEMQQHSWIEVQFLKKAVDVLCQCRATLMYTYVFAFYLKKNNQSIIFENNQADLENATEVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLLQHVHEGYEKDLWEY 554
                                   107       117       127       137       147       157    || 185       195       205       215       225       235       245       255       265       275       285       295       305       315       325   ||  344       354       364       374       384       411       421       431       441      |453       463       473       483       493       503       513       523       533       543       553 
                                                                                          162|                                                                                                                                                 329|                                                  392|                                   448|                                                                                                       
                                                                                           181                                                                                                                                                  339                                                   410                                    451                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhh............hhh.eee.....eeehhhhhhhhhhhh....................hhhhhhh...hhhhhhhhhhhhhhhhhhh.............eeeee......eee.....eee...........hhhhhhhhhhhh..eee......eee......eee........eee....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5udh B  98 DYRYEVLTAEQILQHMVECIREVNEVIQNPATITRILLSHFNWDKEKLMERYFDGMPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILVDDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCGRQFCFNCGENWHDPVKCKWLKKWIKKCDNTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRAALQRYLFYCNRYMNHMQSLRFEHKLYAQVKQKFLKKAVDVLCQCRATLMYTYVFAFYLKKNNQSIIFENNQADLENATEVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLLQHVHEGYEKDLW 552
                                   107       117       127       137       147    || 188       198       208       218       228       238       248       258       268       278       288       298       308       318       328|      349       359       369       379       389 ||    416       426       436    || 461       471       481       491       501       511       521       531       541       551 
                                                                                152|                                                                                                                                             328|                                                391|                             441|                                                                                               
                                                                                 184                                                                                                                                              340                                                 409                              457                                                                                               

Chain C from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...eeeeee.......eeeee...........eeee..............ee................hhhhh........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5udh C   0 SMAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVKLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKR 151
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  

Chain D from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...ee..........eeeeee.....hhhhh.eeeeee..........eeee.............................hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5udh D  -1 GSMAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVKLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPV 153
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148     

Chain E from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeee.....hhhhhhhhhhhhhh.......eee..ee................eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5udh E   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   

   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 5UDH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 46)

Asymmetric Unit(hide GO term definitions)

 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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu B:222 - Glu B:223   [ RasMol ]  
    Pro C:44 - Pro C:45   [ RasMol ]  
    Pro D:44 - Pro D:45   [ RasMol ]  
    Trp A:379 - Glu A:380   [ RasMol ]  
    Trp B:379 - Glu B:380   [ RasMol ]  
    Tyr C:61 - Pro C:62   [ RasMol ]  
    Tyr D:61 - Pro D:62   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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
  5udh
    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
  ARI1_HUMAN | Q9Y4X5
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  Q59EM9_HUMAN | Q59EM9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  UB2L3_HUMAN | P68036
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.2.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
  2.3.2.23
    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
  ARI1_HUMAN | Q9Y4X5
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q59EM9_HUMAN | Q59EM9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  UB2L3_HUMAN | P68036
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ARI1_HUMAN | Q9Y4X51wd2 2m9y 4kbl 4kc9
        UB2L3_HUMAN | P680361c4z 1fbv 3sqv 3sy2 4q5e 4q5h 5hpt

(-) Related Entries Specified in the PDB File

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