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 :  COMPLEX OF PKA WITH THE BISUBSTRATE PROTEIN KINASE INHIBITOR ARC-1408
 
Authors :  A. Pflug, E. Enkvist, A. Uri, R. A. Engh
Date :  25 Mar 16  (Deposition) - 20 Jul 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,E
Keywords :  Protein Kinase, Inhibitor, Bisubstrate, Oligoarginine, Pka, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ivan, E. Enkvist, B. Viira, G. B. Manoharan, G. Raidaru, A. Pflug, K. A. Alam, M. Zaccolo, R. A. Engh, A. Uri
Bifunctional Ligands For Inhibition Of Tight-Binding Protein-Protein Interactions.
Bioconjug. Chem. V. 27 1900 2016
PubMed-ID: 27389935  |  Reference-DOI: 10.1021/ACS.BIOCONJCHEM.6B00293

(-) Compounds

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
    Chains: A
    EC Number: 2.7.11.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRKACA, PKACA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PKA C-ALPHA
 
Molecule 2 - 6J9-ZEU-DAR-ACA-DAR-NH2
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 12)

Asymmetric/Biological Unit (8, 12)
No.NameCountTypeFull Name
16J91OTHER4-(PIPERAZIN-1-YL)-7H-PYRROLO[2,3-D]PYRIMIDINE
2ACA1OTHER6-AMINOHEXANOIC ACID
3AZ11OTHERAZELAIC ACID
4DAR2OTHERD-ARGININE
5NH21OTHERAMINO GROUP
6SEP1Mod. Amino AcidPHOSPHOSERINE
7SO44Ligand/IonSULFATE ION
8TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:257 , LYS A:266 , ARG A:270binding site for residue SO4 A 401
2AC2SOFTWARETRP A:30 , ARG A:93binding site for residue SO4 A 402
3AC3SOFTWAREPRO A:258 , SER A:259 , HIS A:260binding site for residue SO4 A 403
4AC4SOFTWAREILE A:303 , TYR A:306binding site for residue SO4 A 404
5AC5SOFTWAREGLY A:50 , THR A:51 , GLY A:52 , SER A:53 , PHE A:54 , GLY A:55 , ALA A:70 , GLU A:121 , TYR A:122 , VAL A:123 , GLU A:127 , LEU A:173 , THR A:183 , PHE A:327 , DAR E:3 , ACA E:4binding site for residues 6J9 E 1 and AZ1 E 2

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:402 -A:402

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IZF)

(-) 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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh......hhh.eeeeeeeee...eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..............hhhhhhhhhhh..hhhhhhh........................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5izf A  13 ESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWtLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVsINEKCGKEFSEF 350
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192    |  202       212       222       232       242       252       262       272       282       292       302       312       322       332     | 342        
                                                                                                                                                                                                                  197-TPO                                                                                                                                      338-SEP        


Chain E from PDB  Type:OTHER  Length:6
                                      
                 5izf E   1 xxxxxx   6
                            ||||||
                            1-6J9|
                             2-AZ1
                              3-DAR
                               4-ACA
                                5-DAR
                                 6-NH2
   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 5IZF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (77, 77)

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
    6J9  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AZ1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DAR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TPO  [ 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
(no "Cis Peptide Bonds" information available for 5izf)
 

(-) 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
  5izf
    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
  KAPCA_HUMAN | P17612
    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)
  2.7.11.11
    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
  KAPCA_HUMAN | P17612
    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
        KAPCA_HUMAN | P17612: 2gu8 3agl 3agm 3ama 3amb 3l9l 3l9m 3l9n 3mvj 3nx8 3oog 3ovv 3owp 3oxt 3p0m 3poo 3vqh 4ae6 4ae9 4uj1 4uj2 4uj9 4uja 4ujb 4wb5 4wb6 4wb7 4wb8 5bx6 5bx7 5izj 5j5x

(-) Related Entries Specified in the PDB File

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