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 - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  MOLECULAR BASIS FOR PROTEIN RECOGNITION SPECIFICITY OF THE DYNLT1/TCTEX1 CANONICAL BINDING GROOVE. CHARACTERIZATION OF THE INTERACTION WITH ACTIVIN RECEPTOR IIB
 
Authors :  I. Rodriguez-Crespo, J. Merino-Gracia, M. Bruix, H. Zamora-Carreras
Date :  04 May 16  (Deposition) - 17 Aug 16  (Release) - 19 Oct 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Dnylt1/Tctex-1; Dynein Intermediate Chain; Dynein Motor; Dynein- Mediated Transport, Motor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Merino-Gracia, H. Zamora-Carreras, M. Bruix, I. Rodriguez-Cresp
Molecular Basis For The Protein Recognition Specificity Of The Dynein Light Chain Dynlt1/Tctex1: Characterization Of The Interaction With Activin Receptor Iib.
J. Biol. Chem. V. 291 20962 2016
PubMed-ID: 27502274  |  Reference-DOI: 10.1074/JBC.M116.736884

(-) Compounds

Molecule 1 - DYNEIN LIGHT CHAIN TCTEX-TYPE 1,CYTOPLASMIC DYNEIN 1 INTERMEDIATE CHAIN 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-113,UNP RESIDUES 134-154
    Gene: DYNLT1, TCTEL1, TCTEX-1, TCTEX1, DYNC1I2, DNCI2, DNCIC2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: RESIDUES G1 TO S2 CORRESPOND TO THE EXPRESSION TAG. RESIDUES M3 TO I115 CORRESPOND TO THE WHOLE SEQUENCE OF DYNEIN LIGHT CHAIN TCTEX-TYPE 1 (H. SAPIENS, UNIPROT ENTRY P63172). RESIDUES G116 TO S122 CORRESPOND TO A DESIGNED LINKER SEQUENCE. RESIDUES G123 TO V143 CORRESPOND TO RESIDUES G134 TO V154 OF CYTOPLASMIC DYNEIN 1 INTERMEDIATE CHAIN 2 (H. SAPIENS, UNIPROT ENTRY Q13409)
    Synonym: PROTEIN CW-1,T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG, CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 2,DYNEIN INTERMEDIATE CHAIN 2, CYTOSOLIC,DH IC-2

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5JPW)

(-) Sites  (0, 0)

(no "Site" information available for 5JPW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JPW)

(-) 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:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee......eeee.........eeeeeeee...eeeeeeeeee...................eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jpw A   1 GSMEDYQAAEETAFVVDEVSNIVKEAIESAIGGNAYQHSKVNQWTTNVVEQTLSQLTKLGKPFKYIVTCVIMQKNGAGLHTASSCFWDSSTDGSCTVRWENKTMYCIVSAFGLSIGGGSGQSGPIKLGMAKITQVDFPPREIV 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   


Chain B from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee......eeee.........eeeeeeee...eeeeeeeeee...................eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jpw B 144 GSMEDYQAAEETAFVVDEVSNIVKEAIESAIGGNAYQHSKVNQWTTNVVEQTLSQLTKLGKPFKYIVTCVIMQKNGAGLHTASSCFWDSSTDGSCTVRWENKTMYCIVSAFGLSIGGGSGQSGPIKLGMAKITQVDFPPREIV 286
                                   153       163       173       183       193       203       213       223       233       243       253       263       273       283
   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 5JPW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 46)

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
(no "Ligands, Modified Residues, Ions" information available for 5jpw)
 
  Sites
(no "Sites" information available for 5jpw)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5jpw)
 

(-) 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 - 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
  5jpw
    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
  DC1I2_HUMAN | Q13409
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  DYLT1_HUMAN | P63172
    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
  DC1I2_HUMAN | Q13409
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  DYLT1_HUMAN | P63172
    Protein Disorder Prediction: DisEMBL | 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 5JPW)

(-) Related Entries Specified in the PDB File

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