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 :  CRYSTAL STRUCTURE OF DCLK1-KD IN COMPLEX WITH AMPPN
 
Authors :  O. Patel, I. Lucet
Date :  17 May 16  (Deposition) - 24 Aug 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kinase, Doublecortin, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Patel, D. Weiwen, M. Mareike, M. D. W. Griffin, J. Serindoux, Y. Gay, S. Fischer, S. Sterle, A. Kropp, C. J. Burns, M. Ernst, M. Buchert, I. Lucet
Biochemical And Structural Insight Into Doublecortin-Like Kinase Domain 1
Structure V. 24 1 2016
PubMed: search

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE DCLK1
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 372-649
    Gene: DCLK1, DCAMKL1, DCDC3A, KIAA0369
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DOUBLECORTIN DOMAIN-CONTAINING PROTEIN 3A,DOUBLECORTIN-LIKE AND CAM KINASE-LIKE 1,DOUBLECORTIN-LIKE KINASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1AN22Ligand/IonAMP PHOSPHORAMIDATE
2MG2Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1AN21Ligand/IonAMP PHOSPHORAMIDATE
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AN21Ligand/IonAMP PHOSPHORAMIDATE
2MG-1Ligand/IonMAGNESIUM ION
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:516 , ASP A:533 , AN2 A:703 , HOH A:871 , HOH A:921binding site for residue MG A 701
2AC2SOFTWAREARG A:510 , THR A:546 , HOH A:868 , HOH A:874 , HOH A:944 , ARG B:510 , THR B:546binding site for residue SO4 A 702
3AC3SOFTWAREILE A:396 , GLY A:397 , ASP A:398 , GLY A:399 , ASN A:400 , PHE A:401 , ALA A:402 , VAL A:404 , LYS A:419 , VAL A:449 , MET A:465 , GLU A:466 , VAL A:468 , ASP A:472 , GLU A:515 , ASN A:516 , LEU A:518 , ASP A:533 , MG A:701 , HOH A:818 , HOH A:839 , HOH A:843 , HOH A:864 , HOH A:871 , HOH A:893 , HOH A:921 , HOH A:941 , HOH B:1083binding site for residue AN2 A 703
4AC4SOFTWAREASN B:516 , ASP B:533 , AN2 B:902 , HOH B:1100 , HOH B:1134binding site for residue MG B 901
5AC5SOFTWAREARG A:427 , ILE B:396 , GLY B:397 , GLY B:399 , ALA B:402 , VAL B:404 , LYS B:419 , VAL B:449 , MET B:465 , GLU B:466 , VAL B:468 , ASP B:472 , GLU B:515 , ASN B:516 , LEU B:518 , ASP B:533 , MG B:901 , HOH B:1004 , HOH B:1021 , HOH B:1033 , HOH B:1060 , HOH B:1088 , HOH B:1100 , HOH B:1115 , HOH B:1134 , HOH B:1138binding site for residue AN2 B 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:610 -Pro A:611
2Ser B:610 -Pro B:611

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JZJ)

(-) 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhheeeeeeeee...eeeeeeee.....eeeeeeee............hhhhhhh.........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee.....eeeee......ee...............hhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhh............hhhhhhhhhhhh........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jzj A 374 EVSEEGFQIPATITERYKVGRTIGDGNFAVVKECVERSTAREYALKIIKKSKCRGKEHMIQNEVSILRRVKHPNIVLLIEEMDVPTELYLVMELVKGGDLFDAITSTNKYTERDASGMLYNLASAIKYLHSLNIVHRDIKPENLLVYEHQDGSKSLKLGDFGLATIVDGPLYTVCGTPTYVAPEIIAETGYGLKVDIWAAGVITYILLCGFPPFRGSEVLFDQILMGQVDFPSPYWDNVSDSAKELITMMLLVDVDQRFSAVQVLEHPWVN 648
                                   383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583      |597       607       617       627       637       647 
                                                                                                                                                                                                                                                  590|                                                     
                                                                                                                                                                                                                                                   595                                                     


Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhheeeeeeeee...eeeeeeee.....eeeeeeee............hhhhhhh.........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee.....eeeee......ee..........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh......hhhhhhhhh............hhhhhhhhhhhh........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jzj B 382 IPATITERYKVGRTIGDGNFAVVKECVERSTAREYALKIIKKSKCRGKEHMIQNEVSILRRVKHPNIVLLIEEMDVPTELYLVMELVKGGDLFDAITSTNKYTERDASGMLYNLASAIKYLHSLNIVHRDIKPENLLVYEHQDGSKSLKLGDFGLATIVDGPLYTVCGTPTYVAPEIIAETGYGLKVDIWAAGVITYILLCGFPPFREVLFDQILMGQVDFPSPYWDNVSDSAKELITMMLLVDVDQRFSAVQVLEHPWVN 648
                                   391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581      |597       607       617       627       637       647 
                                                                                                                                                                                                                                        588|                                                     
                                                                                                                                                                                                                                         595
   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 5JZJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

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
    AN2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
    Ser A:610 - Pro A:611   [ RasMol ]  
    Ser B:610 - Pro B:611   [ 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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5jzj
    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
  DCLK1_HUMAN | O15075
    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)
  2.7.11.1
    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
  DCLK1_HUMAN | O15075
    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
        DCLK1_HUMAN | O15075: 1mfw 1mg4 1uf0 5jzn

(-) Related Entries Specified in the PDB File

5jzn