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 :  CONFORMATIONAL DYNAMICS OF EXCHANGE PROTEIN DIRECTLY ACTIVATED BY CAMP
 
Authors :  M. A. White, T. N. Tsalkova, F. C. Mei, T. Liu, V. L. Woods, X. Cheng
Date :  16 May 12  (Deposition) - 03 Oct 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyclic Nucleotide, Gef, Exchange Factor, Regulation, Auto-Inhibition, Cdc25 Homology Domain, Exocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. White, S. Li, T. Tsalkova, F. C. Mei, T. Liu, V. L. Woods, X. Cheng
Structural Analyses Of A Constitutively Active Mutant Of Exchange Protein Directly Activated By Camp.
Plos One V. 7 49932 2012
PubMed-ID: 23189173  |  Reference-DOI: 10.1371/JOURNAL.PONE.0049932

(-) Compounds

Molecule 1 - RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SEE REMARK 999
    Gene: RAPGEF4, CGEF2, EPAC2
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: EPAC2, EXCHANGE FACTOR DIRECTLY ACTIVATED BY CAMP 2, EXCHANGE PROTEIN DIRECTLY ACTIVATED BY CAMP 2, EPAC 2, CAMP-DEPENDENT RAP1 GUANINE-NUCLEOTIDE EXCHANGE FACTOR, CAMP-REGULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR II, CAMP-GEFII

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:71 , GLY A:114 , SER A:116 , ARG A:123 , HIS A:124 , ALA A:125 , GOL A:1004BINDING SITE FOR RESIDUE GOL A 1001
2AC2SOFTWAREGLN A:239 , GLY A:242 , MET A:243 , GLY A:305 , PRO A:306 , HIS A:309BINDING SITE FOR RESIDUE GOL A 1002
3AC3SOFTWARESER A:754 , SER A:755 , LYS A:828 , LYS A:831BINDING SITE FOR RESIDUE GOL A 1003
4AC4SOFTWAREPHE A:113 , GLY A:114 , GLU A:115 , SER A:116 , HIS A:124 , TYR A:162 , VAL A:393 , VAL A:394 , GOL A:1001BINDING SITE FOR RESIDUE GOL A 1004
5AC5SOFTWAREARG A:151 , GLN A:152BINDING SITE FOR RESIDUE GOL A 1005
6AC6SOFTWAREPRO A:645 , ARG A:647 , ASN A:771 , CYS A:772 , VAL A:773 , HIS A:774BINDING SITE FOR RESIDUE GOL A 1006
7AC7SOFTWAREHIS A:917 , LYS A:921 , THR A:922BINDING SITE FOR RESIDUE GOL A 1007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F7Z)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:160 -Pro A:161
2Ala A:621 -Pro A:622
3Pro A:900 -Pro A:901

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F7Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F7Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4F7Z)

(-) 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:946
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.....hhhhhhhhhhhhh........hhhhhhhhhhhheeeee....eee.......eeeeeee.eeeeee.........eeeeeee...eehhhhhhh.....eeee...eeeeeeehhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhheeeee..eeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhh..eee............eeee.hhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...eeeee.....eee.......eeeeeee.eeeeee...eeeeeee...ee.hhhhh.......eeee....eeeeeeehhhhhhhhhhhhhheeeee....eeeeee...eeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........ee..............eeeeeee.....eeeeeee...hhhhhhhhhhhhhh....eeeeee.....eee................eeeeee.hhh...............hhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhh............hhhhhhhhhh.....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f7z A  10 QSSAEWIACLDKRPLERSSEDVDIIFTRLKGVKAFEKFHPNLLRQICLCGYYENLEKGITLFRQGDIGTNWYAVLAGSLDVKVSETSSHQDAVTICTLGIGTAFGESILDNTPRHATIVTRESSELLRIEQEDFKALWEKYRQYMAGLLAPPYGVMETGSNNENVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKYLFYRFLDDEREDAPLPTEEEKKECDEELQDTMLLLSQMGPDAHMRMILRKPPGQRTVDDLEIIYDELLHIKALSHLSTTVKRELAGVLIFESHAKGGTVLFNQGEEGTSWYIILKGSVNVVIYGKGVVCTLHEGDDFGKLALVNDAPRAASIVLREDNCHFLRVDKEDGNRILRDVEANTVRLKEHDQDVLVLEKVYTVMSGTPEKILEHFLETIRLEPSLNEATDSVLNDFVMMHCVFMPNTQLCPALVAHYHAQPSQGTEQERMDYALNNKRRVIRLVLQWAAMYGDLLQEDDVAMAFLEEFYVSVSDDARMMAAFKEQLPELEKIVKQISEDAKAPQKKHKRAQKRQPIRGSDEVLFKVYCIDHTYTTIRVPVAASVKEVISAVADKLGSGEGLIIVKMNSGGEKVVLKSNDVSVFTTLTINGRLFACPREQFDSLTPLPEQEGPTTGTVGTFELMSSKDLAYQMTTYDWELFNCVHELELIYHTFGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWEKLPSKFKKFYAEFESLMDPSRNHRAYRLTAAKLEPPLIPFMPLLIKDMTFTHEGNKTFIDNLVNFEKMRMIANTARTVRYYRSQPFNPDAAQKNHQDVRSYVRQLNVIDNQRTLSQMSHRLEPR 991
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 ||    185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455      |482       492       502       512       522       532       542       552       562       572       582       592       602       612       622    || 643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953   ||  965       975       985      
                                                                                                                                                                                           171|                                                                                                                                                                                                                                                                                         462|                                                                                                                                                627|                                                                                                                                                                                                                                                                                                                           957|                               
                                                                                                                                                                                            178                                                                                                                                                                                                                                                                                          480                                                                                                                                                 639                                                                                                                                                                                                                                                                                                                            960
   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 4F7Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F7Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F7Z)

(-) Gene Ontology  (17, 17)

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
    GOL  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:621 - Pro A:622   [ RasMol ]  
    Pro A:160 - Pro A:161   [ RasMol ]  
    Pro A:900 - Pro A:901   [ 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
  4f7z
    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
  RPGF4_MOUSE | Q9EQZ6
    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)
  (no 'Enzyme Classificator' available)
    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
  RPGF4_MOUSE | Q9EQZ6
    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
        RPGF4_MOUSE | Q9EQZ6: 1o7f 2byv 3cf6 4mgi 4mgk 4mgy 4mgz 4mh0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4F7Z)