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 THE CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE DISPLAYING PARTIAL PHOSPHORYL TRANSFER OF AMP-PNP ONTO A SUBSTRATE PEPTIDE
 
Authors :  A. C. Bastidas, J. M. Steichen, J. Wu, S. S. Taylor
Date :  24 Oct 12  (Deposition) - 20 Mar 13  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Protein Kinase Fold, Phosphotransferase, Regulatory Subunits, Pki, Magnesium, Phosphorylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Bastidas, M. S. Deal, J. M. Steichen, Y. Guo, J. Wu, S. S. Taylor
Phosphoryl Transfer By Protein Kinase A Is Captured In A Crystal Lattice.
J. Am. Chem. Soc. V. 135 4788 2013
PubMed-ID: 23458248  |  Reference-DOI: 10.1021/JA312237Q

(-) Compounds

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
    Chains: E
    EC Number: 2.7.11.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRKACA, PKACA
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PKA C-ALPHA
 
Molecule 2 - CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
    Chains: I
    Engineered: YES
    Fragment: SP20 PEPTIDE DERIVED FROM CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA (UNP RESIDUES 6-25)
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: SYNTHETIC PEPTIDE
    Synonym: PKI-ALPHA, CAMP-DEPENDENT PROTEIN KINASE INHIBITOR, MUSCLE/BRAIN ISOFORM
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3MYR1Ligand/IonMYRISTIC ACID
4SEP3Mod. Amino AcidPHOSPHOSERINE
5TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU E:152 , GLU E:155BINDING SITE FOR RESIDUE MYR E 401
2AC2SOFTWAREVAL E:57 , ALA E:70 , LYS E:72 , VAL E:104 , MET E:120 , GLU E:121 , TYR E:122 , VAL E:123 , GLU E:127 , GLU E:170 , ASN E:171 , LEU E:173 , THR E:183 , ASP E:184 , PHE E:327 , MG E:403 , MG E:404 , HOH E:521 , HOH E:596 , HOH E:740 , ARG I:18 , SEP I:21 , HOH I:714BINDING SITE FOR RESIDUE ANP E 402
3AC3SOFTWAREASP E:184 , ANP E:402 , HOH E:595 , SEP I:21 , ANP I:600 , HOH I:714BINDING SITE FOR RESIDUE MG E 403
4AC4SOFTWAREASN E:171 , ASP E:184 , ANP E:402 , HOH E:596 , ANP I:600 , HOH I:747BINDING SITE FOR RESIDUE MG E 404
5AC5SOFTWARELEU E:49 , GLY E:50 , GLY E:52 , VAL E:57 , ALA E:70 , LYS E:72 , VAL E:104 , MET E:120 , GLU E:121 , VAL E:123 , GLU E:127 , LYS E:168 , GLU E:170 , ASN E:171 , LEU E:173 , THR E:183 , ASP E:184 , PHE E:327 , MG E:403 , MG E:404 , HOH E:521 , HOH E:595 , HOH E:596 , ARG I:18 , ALA I:20 , SEP I:21 , HOH I:702 , HOH I:714 , HOH I:729 , HOH I:747 , HOH I:750BINDING SITE FOR RESIDUE ANP I 600
6AC6SOFTWARETHR E:51 , SER E:53 , LEU E:82 , GLN E:84 , GLU E:86 , LEU E:89 , ARG E:93 , GLU E:127 , PHE E:129 , ARG E:133 , LYS E:168 , PRO E:169 , GLU E:170 , ASP E:184 , PHE E:187 , LYS E:189 , ARG E:190 , VAL E:191 , LYS E:192 , LEU E:198 , CYS E:199 , GLY E:200 , THR E:201 , GLU E:203 , GLU E:230 , TYR E:235 , PRO E:236 , PHE E:239 , ALA E:240 , ASP E:241 , ILE E:246 , TYR E:330 , GLU E:349 , ANP E:402 , MG E:403 , HOH E:514 , HOH E:518 , HOH E:592 , HOH E:595 , HOH E:728 , HOH E:882 , ANP I:600 , HOH I:701 , HOH I:703 , HOH I:704 , HOH I:705 , HOH I:706 , HOH I:707 , HOH I:708 , HOH I:709 , HOH I:710 , HOH I:711 , HOH I:712 , HOH I:713 , HOH I:714 , HOH I:715 , HOH I:716 , HOH I:717 , HOH I:718 , HOH I:719 , HOH I:720 , HOH I:721 , HOH I:723 , HOH I:726 , HOH I:729 , HOH I:731 , HOH I:732 , HOH I:735 , HOH I:737 , HOH I:740 , HOH I:742 , HOH I:744 , HOH I:746 , HOH I:747 , HOH I:748 , HOH I:749 , HOH I:750BINDING SITE FOR CHAIN I OF CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HPU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HPU)

(-) 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 E from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh......hhh.eeeeeeeee...eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........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
                 4hpu E  12 QESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFsEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWtLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVsINEKCGKEFTEF 350
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     | 201       211       221       231       241       251       261       271       281       291       301       311       321       331      |341         
                                                                                                                                                         139-SEP                                                   197-TPO                                                                                                                                      338-SEP        


Chain I from PDB  Type:PROTEIN  Length:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 4hpu I   5 TTYADFIASGRTGRRAsIH  23
                                    14      |  
                                           21-SEP
   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 4HPU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (70, 72)

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
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MYR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hpu)
 

(-) 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
  4hpu
    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
  IPKA_MOUSE | P63248
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  KAPCA_MOUSE | P05132
    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
  IPKA_MOUSE | P63248
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  KAPCA_MOUSE | P05132
    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
        IPKA_MOUSE | P63248: 1apm 1atp 1jbp 1jlu 1l3r 1pvk 2cpk 2gnf 2gng 2qur 3fjq 3ow3 3qal 3qam 3zo2 4dfx 4dfz 4dg0 4dg2 4dg3 4dh1 4dh3 4dh5 4dh7 4dh8 4hpt
        KAPCA_MOUSE | P05132: 1apm 1atp 1bkx 1bx6 1fmo 1j3h 1jbp 1jlu 1l3r 1pvk 1rdq 1re8 1rej 1rek 1syk 2cpk 2erz 2qcs 2qur 2qvs 3fhi 3fjq 3idb 3idc 3j4q 3j4r 3o7l 3ow3 3pvb 3qal 3qam 3tnp 3tnq 3x2u 3x2v 3x2w 4dfx 4dfy 4dfz 4dg0 4dg2 4dg3 4dh1 4dh3 4dh5 4dh7 4dh8 4din 4hpt 4iac 4iad 4iaf 4iai 4iak 4iay 4iaz 4ib0 4ib1 4ib3 4nts 4ntt 4o21 4o22 4wbb 4x6q 4x6r 4xw4 4xw5 4xw6 5jr7 5x3f

(-) Related Entries Specified in the PDB File

4hpt SAME COMPLEX DISPLAYING COMPLETE PHOSPHORYL TRANSFER