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 UCH-L5 IN COMPLEX WITH INHIBITORY FRAGMENT OF INO80G
 
Authors :  D. D. Sahtoe, W. J. Van Dijk, F. El Oualid, R. Ekkebus, H. Ovaa, T. K. Six
Date :  23 Dec 14  (Deposition) - 04 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Deubiquitinating Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. D. Sahtoe, W. J. Van Dijk, F. El Oualid, R. Ekkebus, H. Ovaa, T. K. Sixma
Mechanism Of Uch-L5 Activation And Inhibition By Deubad Domains In Rpn13 And Ino80G.
Mol. Cell V. 57 887 2015
PubMed-ID: 25702870  |  Reference-DOI: 10.1016/J.MOLCEL.2014.12.039

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5
    Chains: A
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-NKI-3C-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector: PGEX VECTOR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: ISOFORM 3
    Synonym: UCH-L5, UBIQUITIN C-TERMINAL HYDROLASE UCH37, UBIQUITIN THIOESTERASE L5, UCH-L5
 
Molecule 2 - NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-NKI-HIS-3C-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector: PET VECTOR
    Fragment: DEUBAD DOMAIN, RESIDUES 40-170
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA-BINDING PROTEIN R KAPPA-B, INO80 COMPLEX SUBUNIT G, INO 80G

 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 4UF5)

(-) Sites  (0, 0)

(no "Site" information available for 4UF5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UF5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:47 -Pro A:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UF5)

(-) Exons   (0, 0)

(no "Exon" information available for 4UF5)

(-) 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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh....eeeee....hhhhhhh...eeeeeeee...............hhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee..eeeeee......eeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uf5 A   6 GEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLASMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQN 320
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145 ||    167       177       187       197       207       217       227       237     ||257       267       277       287       297       307       317   
                                                                                                                                                                       147|                                                                                243|                                                                  
                                                                                                                                                                        160                                                                                 254                                                                  


Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 4uf5 B  44 EDPEIFFDVVSLSTWQEVLSDSQREHLQQFLPQFPEDSAEQQNELILALFSGENFRFGNPLHIAQKLFRDGHFNPEVVKYRQLCFKSQYKRYLNSQQQYFHRLLKQILAS 153
                                    53        63        73        83        93       103       113       123       133       143       153
   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 4UF5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UF5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UF5)

(-) Gene Ontology  (32, 40)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4uf5)
 
  Sites
(no "Sites" information available for 4uf5)
 
  Cis Peptide Bonds
    Lys A:47 - Pro A:48   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4uf5
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NFRKB_HUMAN | Q6P4R8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  UCHL5_HUMAN | Q9Y5K5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.19.12
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NFRKB_HUMAN | Q6P4R8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  UCHL5_HUMAN | Q9Y5K5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NFRKB_HUMAN | Q6P4R8: 3u21 4uf6 4wlp
        UCHL5_HUMAN | Q9Y5K5: 3a7s 3ihr 3rii 3ris 3tb3 4uel 4uem 4uf6 4wlp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4UF5)