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 RSK2 CTD BOUND TO 3-(3-(1H-PYRROLO[2,3-B]PYRIDINE-3-CARBONYL)PHENYL)-2-CYANOACRYLAMIDE
 
Authors :  R. M. Miller, V. O. Paavilainen, S. Krishnan, I. M. Serafimova, J. Taunt
Date :  28 Feb 13  (Deposition) - 10 Apr 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinase, Phosphorylation, Covalent Inhibitor, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Miller, V. O. Paavilainen, S. Krishnan, I. M. Serafimova, J. Taunton
Electrophilic Fragment-Based Design Of Reversible Covalent Kinase Inhibitors.
J. Am. Chem. Soc. V. 135 5298 2013
PubMed-ID: 23540679  |  Reference-DOI: 10.1021/JA401221B

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN S6 KINASE ALPHA-3
    Chains: A
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RPS6KA3, ISPK1, MAPKAPK1B, RSK2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: S6K-ALPHA-3, 90 KDA RIBOSOMAL PROTEIN S6 KINASE 3, P90-RSK 3, P90RSK3, INSULIN-STIMULATED PROTEIN KINASE 1, ISPK-1, MAP KINASE- ACTIVATED PROTEIN KINASE 1B, MAPK-ACTIVATED PROTEIN KINASE 1B, MAPKAP KINASE 1B, MAPKAPK-1B, RIBOSOMAL S6 KINASE 2, RSK-2, PP90RSK2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
11LC1Ligand/Ion(2R)-2-CYANO-3-[3-(1H-PYRROLO[2,3-B]PYRIDIN-3-YLCARBONYL)PHENYL]PROPANAMIDE
2NA1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:428 , CYS A:436 , ALA A:449 , LYS A:451 , THR A:493 , MET A:496 , LEU A:546 , ASP A:561 , HOH A:914BINDING SITE FOR RESIDUE 1LC A 801
2AC2SOFTWAREGLY A:471 , HIS A:473 , PRO A:474 , ILE A:476 , THR A:478BINDING SITE FOR RESIDUE NA A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JG7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JG7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JG7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JG7)

(-) Exons   (0, 0)

(no "Exon" information available for 4JG7)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhh.eeeeee......eeeeee.....eeeeeeee.....hhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....hhh.eee......ee..................hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jg7 A 405 HSIVQQLHRNSIQFTDGYEVKEDIGVYSVCKRCIHKATNMEFAVKIIDKSKRDPTEEIEILLRYGQHPNIITLKDVYDDGKYVYVVTELMKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNPESIRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLERQGYDAACDIWSLGVLLYTMLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAKDLVSKMLHVDPHQRLTAALVLRHPWIVHWDQLPQYQLNRQDAPHLVKGAMAATYSALNRN 713
                                   414       424     ||436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       
                                                   430|                                                                                                                                                                                                                                                                                        
                                                    433
   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 4JG7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JG7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JG7)

(-) Gene Ontology  (31, 31)

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
    1LC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jg7)
 

(-) 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
  4jg7
    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
  KS6A3_HUMAN | P51812
    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)
  2.7.11.1
    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
  KS6A3_HUMAN | P51812
    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
        KS6A3_HUMAN | P51812: 4d9t 4d9u 4jg6 4jg8 4nus 4nw5 4nw6 5d9k 5d9l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JG7)