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 :  STRUCTURE OF CAMP DEPENDENT PROTEIN KINASE A IN COMPLEX WITH HIGH K+ CONCENTRATION, ADP AND PHOSPHORYLATED PEPTIDE PSP20
 
Authors :  O. Gerlits, A. Kovalevsky
Date :  07 Dec 12  (Deposition) - 11 Dec 13  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A,S
Keywords :  Kinase Enzyme, Phosphotransfer, Phosphorylated, Transferase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Gerlits, A. Das, M. M. Keshwani, S. Taylor, M. J. Waltman, P. Langan, W. T. Heller, A. Kovalevsky
Metal-Free Camp-Dependent Protein Kinase Can Catalyze Phosphoryl Transfer.
Biochemistry V. 53 3179 2014
PubMed-ID: 24786636  |  Reference-DOI: 10.1021/BI5000965

(-) 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: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PKA C-ALPHA
 
Molecule 2 - PHOSPHORYLATED PSEUDO-SUBSTRATE PEPTIDE PSP20
    Chains: S
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2K2Ligand/IonPOTASSIUM ION
3SEP3Mod. Amino AcidPHOSPHOSERINE
4TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:184 , ADP A:403 , HOH A:1002 , HOH A:1003 , SEP S:621 , HOH S:703BINDING SITE FOR RESIDUE K A 401
2AC2SOFTWAREASN A:171 , ASP A:184 , ADP A:403 , HOH A:1001 , SEP S:621 , HOH S:701 , HOH S:702BINDING SITE FOR RESIDUE K A 402
3AC3SOFTWAREGLY A:50 , GLY A:52 , GLY A:55 , VAL A:57 , ALA A:70 , LYS A:72 , VAL A:104 , MET A:120 , GLU A:121 , TYR A:122 , VAL A:123 , GLU A:127 , GLU A:170 , ASN A:171 , LEU A:173 , THR A:183 , ASP A:184 , PHE A:327 , K A:401 , K A:402 , HOH A:1001 , HOH A:1003 , HOH A:1150 , HOH A:1161 , ARG S:618 , SEP S:621 , HOH S:701BINDING SITE FOR RESIDUE ADP A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IB1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IB1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IB1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IB1)

(-) Exons   (0, 0)

(no "Exon" information available for 4IB1)

(-) 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 hhhhhhhhhhhhhhhhhhhh......hhh.eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee........eehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..............hhhhhhhhhhh..hhhhhhh........................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ib1 A  13 ESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFsEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWtLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVsINEKCGKEFTEF 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        
                                                                                                                                                        139-SEP                                                   197-TPO                                                                                                                                      338-SEP        


Chain S from PDB  Type:PROTEIN  Length:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .hhhhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 4ib1 S 605 TTYADFIASGRTGRRAsIHD 624
                                   614      |624
                                          621-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 4IB1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IB1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IB1)

(-) Gene Ontology  (70, 73)

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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ib1)
 

(-) 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
  4ib1
    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_HUMAN | P61925
    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_HUMAN | P61925
    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_HUMAN | P61925: 1cdk 1cmk 1ctp 1jlu 1q24 1q61 1q62 1q8t 1q8u 1q8w 1smh 1stc 1sve 1svg 1svh 1veb 1xh4 1xh5 1xh6 1xh7 1xh8 1xh9 1xha 1ydr 1yds 1ydt 2c1a 2c1b 2f7e 2gni 2jds 2jdt 2jdv 2l1l 2uvx 2uvy 2uvz 2uw0 2uw3 2uw4 2uw5 2uw6 2uw7 2uw8 2vnw 2vny 2vo0 2vo3 2vo6 2vo7 3ama 3amb 3l9l 3l9m 3l9n 3mvj 3nx8 3oog 3ovv 3owp 3oxt 3p0m 3poo 3vqh 3wyg 3x2u 3x2v 3x2w 4axa 4iac 4iad 4iaf 4iai 4iak 4iay 4iaz 4ib0 4ib3 4ie9 4ij9 4o21 4o22 4uj1 4uj2 4uj9 4uja 4ujb 4wb5 4wb6 4wb7 4wb8 4z83 4z84 5bx6 5bx7 5dh9
        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 4hpu 4iac 4iad 4iaf 4iai 4iak 4iay 4iaz 4ib0 4ib3 4nts 4ntt 4o21 4o22 4wbb 4x6q 4x6r 4xw4 4xw5 4xw6 5jr7 5x3f

(-) Related Entries Specified in the PDB File

4iac 4iad 4iaf 4iai 4iak 4iay 4iaz 4ib0 4ib3