Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  SELECTIVE ACTIVATION OF EPAC1 AND EPAC2
 
Authors :  H. Rehmann
Date :  29 Aug 13  (Deposition) - 03 Sep 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  E,R
Biol. Unit 1:  E,R  (1x)
Biol. Unit 2:  E,R  (2x)
Keywords :  Guanine Nucleotide Exchange Factor, Nucleotide Binding, Signaling Protein-Gtp-Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Rehmann
Selective Activation Of Epac1 And Epac2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T1
    Expression System Strain: CK600K
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 324-1011
    Gene: RAPGEF4, CGEF2, EPAC2
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: 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
 
Molecule 2 - RAS-RELATED PROTEIN RAP-1B
    Chains: R
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTAC
    Expression System Strain: CK600K
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-169
    Gene: RAP1B, OK/SW-CL.11
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GTP-BINDING PROTEIN SMG P21B

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : ER
Biological Unit 1 (1x): ER
Biological Unit 2 (2x): ER

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1H071Ligand/Ion(2S,4AR,6R,7R,7AR)-6-{6-AMINO-8-[(4-CHLOROPHENYL)SULFANYL]-9H-PURIN-9-YL}-7-METHOXYTETRAHYDRO-4H-FURO[3,2-D][1,3,2]DIOXAPHOSPHININ-2-OL 2-OXIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1H071Ligand/Ion(2S,4AR,6R,7R,7AR)-6-{6-AMINO-8-[(4-CHLOROPHENYL)SULFANYL]-9H-PURIN-9-YL}-7-METHOXYTETRAHYDRO-4H-FURO[3,2-D][1,3,2]DIOXAPHOSPHININ-2-OL 2-OXIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1H072Ligand/Ion(2S,4AR,6R,7R,7AR)-6-{6-AMINO-8-[(4-CHLOROPHENYL)SULFANYL]-9H-PURIN-9-YL}-7-METHOXYTETRAHYDRO-4H-FURO[3,2-D][1,3,2]DIOXAPHOSPHININ-2-OL 2-OXIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE E:367 , ILE E:388 , VAL E:394 , ASP E:402 , GLY E:404 , GLN E:405 , LEU E:406 , ALA E:407 , ARG E:414 , ALA E:415 , ARG E:448 , LEU E:449 , LYS E:450 , GLU E:451 , LYS E:489 , HOH E:1122 , HOH E:1185BINDING SITE FOR RESIDUE H07 E 1001
2AC2SOFTWARESER R:11 , GLY R:12 , GLY R:13 , VAL R:14 , GLY R:15 , LYS R:16 , SER R:17 , ALA R:59 , HOH R:307BINDING SITE FOR RESIDUE SO4 R 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MGY)

(-) Sequences/Alignments

Asymmetric 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:627
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..eeeee.....eee.......eeeeeee..eeeee...eeeeee....eehhhhhhhh.....eeee....eeeeeeehhhhhhhh......eeeeee..eeeeeeee...eeeeeehhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh........eeeeeee.....eeeeeee...hhhhhhhhhhhhhh....eeeeee.....eee.......hhhhh....eeeeee.hhhhhh..hhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...ee..eeehhhhhhhhhhhhhhhhhh......hhhhhhhh......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mgy E 310 MRMILRKPPGQRTVDDLEIIYDELLHIKALSHLSTTVKRELAGVLIFESHAKGGTVLFNQGEEGTSWYIILKGSVNVVIYGKGVVCTLHEGDDFGQLALVNDAPRAASIVLREDNCHFLRVDKEDFNRILRDVEANTVRLKEHDQDVLVLEKVQKYTVMSGTPEKILEHFLETIRLEPSLNEATDSVLNDFVMMHCVFMPNTQLCPALVAHYHAQPSQGTEQERMDYALNNKRRVIRLVLQWAAMYGDLLQEDDVAMAFLEEFYVSVSDDARMMAAFKEQLPELEKIVRQPIRGSDEVLFKVYCIDHTYTTIRVPVAASVKEVISAVADKLGSGEGLIIVKMNSGGEKVVLKSNDVSVFTTLTINGRLFACPREQFDSLTPLPEQEGPTTGTVGTFELMSSKDLAYQMTTYDWELFNCVHELELIYHTFGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWEKLPSKFKKFYAEFESLMDPSRNHRAYRLTAAKLEPPLIPFMPLLIKDMTFTHEGNKTFIDNLVNFEKMRMIANTARTVRYYRSQPFNHQDVRSYVRQLNVIDNQRTLSQMSHRLEP 990
                                   319       329       339       349       359       369       379       389       399       409       419       429       439       449       459  ||   484       494       504       514       524       534       544       554       564       574       584       594       604       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       963       973       983       
                                                                                                                                                                                  462|                                                                                                                                   612|                                                                                                                                                                                                                                                                                                                  952|                            
                                                                                                                                                                                   478                                                                                                                                    643                                                                                                                                                                                                                                                                                                                   962                            


Chain R from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...............eee...eeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee...........hhhhhhh.ee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mgy R   3 EYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLAFLESSAKSKINVNEIFYDLVRQ 164
                                    12        22        32        42 ||     57        67        77        87        97       107       117       127      |144       154       164
                                                                    44|                                                                                 134|                      
                                                                     50                                                                                  142
   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 4MGY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 41)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    H07  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4mgy)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4mgy
    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
  RAP1B_HUMAN | P61224
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  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
  RAP1B_HUMAN | P61224
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  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
        RAP1B_HUMAN | P61224: 3brw 3cf6 4dxa 4hdo 4hdq 4m8n 4mgi 4mgk 4mgz 4mh0 5kho
        RPGF4_MOUSE | Q9EQZ6: 1o7f 2byv 3cf6 4f7z 4mgi 4mgk 4mgz 4mh0

(-) Related Entries Specified in the PDB File

2byv INACTIVE EPAC2
3cf6 COMPLEX WITH SP1 / SP-CAMPS / 6-(6-AMINO-PURIN-9-YL)-2- THIOXO-TETRAHYDRO-2-FURO[3,2- D][1,3,2]DIOXAPHOSPHININE-2, 7-DIOL / SP-ADENOSINE-3',5'-CYCLIC-MONOPHOSPHOROTHIOATE
4mgi COMPLEX WITH CMP / CAMP / CYCLIC AMP / ADENOSINE-3',5'- CYCLIC-MONOPHOSPHATE
4mgk COMPLEX OF MUTANT K405Q WITH CMP / CAMP / CYCLIC AMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
4mgz COMPLEX WITH SP-8-BNT-CAMPS / 8-BENZYLTHIOADENOSINE-3',5'- CYCLIC MONOPHOSPHOROTHIOATE, SP-ISOMER
4mh0