Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF NDP52 UBIQUITIN-BINDING ZINC FINGER
 
Authors :  L. Pan, X. Xie
Date :  12 Jan 15  (Deposition) - 11 Nov 15  (Release) - 11 Nov 15  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Zinc Finger, Ndp52, Ubiquitin-Binding, C2H2-Type, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xie, F. Li, Y. Wang, Y. Wang, Z. Lin, X. Cheng, J. Liu, C. Chen, L. Pan
Molecular Basis Of Ubiquitin Recognition By The Autophagy Receptor Calcoco2
Autophagy V. 11 1775 2015
PubMed-ID: 26506893  |  Reference-DOI: 10.1080/15548627.2015.1082025

(-) Compounds

Molecule 1 - CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET32A
    Fragment: C-TERMINAL, UNP RESIDUES 414-446
    Gene: CALCOCO2, NDP52
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANTIGEN NUCLEAR DOT 52 KDA PROTEIN, NUCLEAR DOMAIN 10 PROTEIN NDP52, NUCLEAR DOMAIN 10 PROTEIN 52, NUCLEAR DOT PROTEIN 52

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:57 , CYS A:60 , HIS A:75 , HIS A:79BINDING SITE FOR RESIDUE ZN A 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MXP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MXP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2MXP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2MXP)

(-) Exons   (0, 0)

(no "Exon" information available for 2MXP)

(-) Sequences/Alignments

NMR Structure
   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:33
                                                                
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author .....eee......eee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                  2mxp A 49 QMQPLCFNCPICDKIFPATEKQIFEDHVFCHSL 81
                                    58        68        78
   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 2MXP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MXP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MXP)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)

 Visualization

(-) Interactive Views

NMR Structure
  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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2mxp)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  2mxp
    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
  CACO2_HUMAN | Q13137
    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)
  (no 'Enzyme Classificator' available)
    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
  CACO2_HUMAN | Q13137
    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
        CACO2_HUMAN | Q13137: 3vvv 3vvw 4gxl 4han 4xkl 5aaq

(-) Related Entries Specified in the PDB File

4xkl RELATED ID: 25423 RELATED DB: BMRB