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

(-) Description

Title :  STRUCTURAL BASIS FOR THE INDISPENSABLE ROLE OF A UNIQUE ZINC FINGER MOTIF IN LNX2 UBIQUITINATION
 
Authors :  J. Sivaraman, D. Nayak
Date :  01 Sep 15  (Deposition) - 14 Oct 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  E3 Ligase, Ubiquitination, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Nayak, J. Sivaraman
Structural Basis For The Indispensable Role Of A Unique Zin Finger Motif In Lnx2 Ubiquitination.
Oncotarget V. 6 34342 2015
PubMed-ID: 26451611  |  Reference-DOI: 10.18632/ONCOTARGET.5326

(-) Compounds

Molecule 1 - LIGAND OF NUMB PROTEIN X 2
    Chains: A, B
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 20-147
    Gene: LNX2, PDZRN1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUMB-BINDING PROTEIN 2,PDZ DOMAIN-CONTAINING RING FINGER PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2ZN8Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:31 , CYS A:34 , CYS A:51 , CYS A:54binding site for residue ZN A 201
2AC2SOFTWARECYS A:46 , HIS A:48 , CYS A:65 , ASP A:68binding site for residue ZN A 202
3AC3SOFTWARECYS A:4 , CYS A:7 , HIS A:11 , HIS A:17binding site for residue ZN A 203
4AC4SOFTWARECYS A:95 , CYS A:101 , HIS A:113 , CYS A:118binding site for residue ZN A 204
5AC5SOFTWARECYS B:95 , CYS B:101 , HIS B:113 , CYS B:118binding site for residue ZN B 201
6AC6SOFTWARECYS B:4 , CYS B:7 , HIS B:11 , HIS B:17binding site for residue ZN B 202
7AC7SOFTWARECYS B:31 , CYS B:34 , CYS B:51 , CYS B:54binding site for residue ZN B 203
8AC8SOFTWARECYS B:46 , HIS B:48 , CYS B:65 , ASP B:68binding site for residue ZN B 204
9AC9SOFTWARETRP A:12 , THR A:13 , ARG A:14 , HOH A:336 , ASN B:16 , ASN B:57 , HOH B:338 , HOH B:399binding site for residue MES B 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DIN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DIN)

(-) 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:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................ee....hhhhh..........eee.....eeehhhhhhhh.............hhhhhee.hhhhhhhhhh.eee.........eee..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 5din A   2 PLCFECGQQHWTRENHLYNYQNEVDDDLVCHICLQPLLQPLDTPCGHTFCYKCLRNFLQEKDFCPLDRKRLHFKLCKKSSILVHKLLDKLLVLCPFSSVCKDVMQRCDLEAHLKNRCPGA 121
                                    11        21        31        41        51        61        71        81        91       101       111       121


Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................ee....hhhhh..........eee.....eeehhhhhhhh.............hhhhhee.hhhhhhhhhh.eee.........eee..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5din B  -1 EFNPLCFECGQQHWTRENHLYNYQNEVDDDLVCHICLQPLLQPLDTPCGHTFCYKCLRNFLQEKDFCPLDRKRLHFKLCKKSSILVHKLLDKLLVLCPFSSVCKDVMQRCDLEAHLKNRCPGAS 122
                                     8        18        28        38        48        58        68        78        88        98       108       118
   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 5DIN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

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
    MES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5din)
 

(-) 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 | Asym./Biol. Unit - sites 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
  5din
    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
  LNX2_HUMAN | Q8N448
    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)
  6.3.2.19
    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
  LNX2_HUMAN | Q8N448
    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
        LNX2_HUMAN | Q8N448: 2vwr 5e11 5e1y 5e21 5e22

(-) Related Entries Specified in the PDB File

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