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 :  CRYSTAL STRUCTURE OF PRK1 CATALYTIC DOMAIN IN COMPLEX WITH TOFACITINIB
 
Authors :  P. P. Chamberlain, S. Delker, Pagarigan B. , A. Mahmoudi, P. Jackson, M. Abbassian, J. Muir, N. Raheja, B. Cathers
Date :  13 Feb 14  (Deposition) - 27 Aug 14  (Release) - 27 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Prk1, Pkn1, Protein Kinase C Related Kinase 1, Kinase, Protein Kinase, Atp Binding, Phosphorylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Chamberlain, S. Delker, B. Pagarigan, A. Mahmoudi, P. Jackson, M. Abbasian, J. Muir, N. Raheja, B. Cathers
Crystal Structures Of Prk1 In Complex With The Clinical Compounds Lestaurtinib And Tofacitinib Reveal Ligand Induce Conformational Changes.
Plos One V. 9 03638 2014
PubMed-ID: 25111382  |  Reference-DOI: 10.1371/JOURNAL.PONE.0103638

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE N1
    Chains: A
    EC Number: 2.7.11.13
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 605-942
    Gene: PKN1, PAK1, PKN, PRK1, PRKCL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEASE-ACTIVATED KINASE 1, PAK-1, PROTEIN KINASE C-LIKE 1, PROTEIN KINASE C-LIKE PKN, PROTEIN KINASE PKN-ALPHA, PROTEIN-KINASE C-RELATED KINASE 1, SERINE-THREONINE PROTEIN KINASE N

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MI11Ligand/Ion3-{(3R,4R)-4-METHYL-3-[METHYL(7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)AMINO]PIPERIDIN-1-YL}-3-OXOPROPANENITRILE
2SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:627 , GLY A:628 , ARG A:629 , GLY A:630 , GLY A:633 , LYS A:634 , VAL A:635 , ALA A:648 , GLU A:702 , SER A:704 , ASP A:750 , LEU A:753 , ASP A:764 , PHE A:910BINDING SITE FOR RESIDUE MI1 A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:883 -Gly A:884

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OTI)

(-) 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:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeeeeeeee...eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeeee...eeeeeee.....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhhhh....................hhhhhh..............hhhhhhh.....ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oti A 612 RKSPLTLEDFKFLAVLGRGHFGKVLLSEFRPSGELFAIKALKKGDIVARDEVESLMCEKRILAAVTSAGHPFLVNLFGCFQTPEHVCFVMEYSAGGDLMLHIHSDVFSEPRAIFYSACVVLGLQFLHEHKIVYRDLKLDNLLLDTEGYVKIADFGLTRAVDWWGLGVLLYEMLVGESPFPGDDEEEVFDSIVNDEVRYPRFLSAEAIGIMRRLLRRNPERRLGSSERDAEDVKKQPFFRTLGWEALLARRLPPPFVPTLSGRTDVSNFDEEFTGEAPTLsPPRDARPLTAAEQAAFLDFDFVAG 946
                                   621       631       641       651       661       671       681       691       701       711       721       731       741       751       761     ||802       812       822       832       842       852       862       872       882       892       902       912       922       932       942    
                                                                                                                                                                                     767|                                                                                                                        922-SEP                    
                                                                                                                                                                                      799
   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 4OTI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 48)

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
    MI1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:883 - Gly A:884   [ 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 | 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
  4oti
    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
  PKN1_HUMAN | Q16512
    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)
  2.7.11.13
    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
  PKN1_HUMAN | Q16512
    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
        PKN1_HUMAN | Q16512: 1cxz 1urf 2rmk 4nkg 4otd 4otg 4oth

(-) Related Entries Specified in the PDB File

4otd 4otg 4oth