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 :  THE CRYSTAL STRUCTURE OF H-RAS AND SOS IN COMPLEX WITH LIGANDS
 
Authors :  J. J. G. Winter, M. Anderson, K. Blades, C. Brassington, A. L. Breeze, C. K. Embrey, G. Fairley, P. Faulder, M. R. V. Finlay, J. G. Kettle, T. Nowa R. Overman, S. J. Patel, P. Perkins, L. Spadola, J. Tart, J. Tucker, G. W
Date :  02 Jul 14  (Deposition) - 04 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  R,S
Keywords :  Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Winter, M. Anderson, K. Blades, C. Chresta, K. J. Embrey, G. Fairley P. Faulder, M. R. V. Finlay, J. G. Kettle, T. Nowak, R. Overman, S. J. Patel, P. Perkins, L. Spadola, J. Tart, J. A. Tucker, G. Wrigley
Small Molecule Binding Sites On The Ras:Sos Complex Can Be Exploited For Inhibition Of Ras Activation.
J. Med. Chem. V. 58 2265 2015
PubMed-ID: 25695162  |  Reference-DOI: 10.1021/JM501660T

(-) Compounds

Molecule 1 - GTPASE HRAS
    Chains: R
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-166
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: H-RAS-1, HA-RAS, TRANSFORMING PROTEIN P21, C-H-RAS, P21RAS, H-RAS
 
Molecule 2 - SON OF SEVENLESS HOMOLOG 1
    Chains: S
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 564-1049
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SOS-1, SON OF SEVENLESS-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : RS

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1VJP1Ligand/Ion1-[(4-AMINOPHENYL)SULFONYL]PIPERIDIN-2-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS R:5 , LEU R:6 , ASP R:54 , LEU R:56 , THR R:74 , SER S:908 , GLU S:909 , ASP S:910 , HIS S:911 , TYR S:912BINDING SITE FOR RESIDUE VJP R1167

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro S:924 -Pro S:925
2Asn S:1020 -Pro S:1021

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4URZ)

(-) 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 R from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee......hhhhhhhhh..........hhhh.eeeeee..eeeeeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4urz R    0 HMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH  166
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       


Chain S from PDB  Type:PROTEIN  Length:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh......eeeeeee......eeeeeehhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh................hhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...eeee..eeeeehhhhhhhhhhhhhhhhh.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4urz S  567 MRLPSADVYRFAEPDSEENIIFEENMQPKAGIPIIKAGTVIKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPLSAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIAFQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQPYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSNP 1045
                                   576       586       596       606       616       626       636       646       670       680       690       700       710       720       730       740  ||   760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040     
                                                                                                                  655|                                                                      743|                                                                                                                                                                                                                                                                                                   
                                                                                                                   670                                                                       754
   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 4URZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (97, 110)

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
    VJP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn S:1020 - Pro S:1021   [ RasMol ]  
    Pro S:924 - Pro S:925   [ 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
  4urz
    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
  RASH_HUMAN | P01112
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SOS1_HUMAN | Q07889
    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
  RASH_HUMAN | P01112
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SOS1_HUMAN | Q07889
    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
        RASH_HUMAN | P01112: 121p 1aa9 1agp 1bkd 1clu 1crp 1crq 1crr 1ctq 1gnp 1gnq 1gnr 1he8 1iaq 1ioz 1jah 1jai 1k8r 1lf0 1lf5 1lfd 1nvu 1nvv 1nvw 1nvx 1p2s 1p2t 1p2u 1p2v 1plj 1plk 1pll 1q21 1qra 1rvd 1wq1 1xcm 1xd2 1xj0 1zvq 1zw6 221p 2c5l 2ce2 2cl0 2cl6 2cl7 2clc 2cld 2evw 2gdp 2lcf 2lwi 2n42 2n46 2q21 2quz 2rga 2rgb 2rgc 2rgd 2rge 2rgg 2uzi 2vh5 2x1v 3ddc 3i3s 3k8y 3k9l 3k9n 3kkm 3kkn 3kud 3l8y 3l8z 3lbh 3lbi 3lbn 3lo5 3oiu 3oiv 3oiw 3rry 3rrz 3rs0 3rs2 3rs3 3rs4 3rs5 3rs7 3rsl 3rso 3tgp 421p 4dlr 4dls 4dlt 4dlu 4dlv 4dlw 4dlx 4dly 4dlz 4dst 4dsu 4efl 4efm 4efn 4g0n 4g3x 4k81 4l9s 4l9w 4nyi 4nyj 4nym 4q21 4rsg 4uru 4urv 4urw 4urx 4ury 4us0 4us1 4us2 4xvq 4xvr 521p 5b2z 5b30 5e95 5p21 621p 6q21 721p 821p
        SOS1_HUMAN | Q07889: 1awe 1bkd 1dbh 1nvu 1nvv 1nvw 1nvx 1q9c 1xd2 1xd4 1xdv 2ii0 3ksy 4nyi 4nyj 4nym 4uru 4urv 4urw 4urx 4ury 4us0 4us1 4us2

(-) Related Entries Specified in the PDB File

4uru THE CRYSTAL STRUCTURE OF H-RAS AND SOS IN COMPLEX WITH LIGANDS
4urv THE CRYSTAL STRUCTURE OF H-RAS AND SOS IN COMPLEX WITH LIGANDS
4urw THE CRYSTAL STRUCTURE OF H-RAS AND SOS IN COMPLEX WITH LIGANDS
4urx THE CRYSTAL STRUCTURE OF H-RAS AND SOS IN COMPLEX WITH LIGANDS
4ury THE CRYSTAL STRUCTURE OF H-RAS AND SOS IN COMPLEX WITH LIGANDS
4us0 THE CRYSTAL STRUCTURE OF H-RAS AND SOS IN COMPLEX WITH LIGANDS
4us1 THE CRYSTAL STRUCTURE OF H-RAS AND SOS IN COMPLEX WITH LIGANDS
4us2 THE CRYSTAL STRUCTURE OF H-RAS AND SOS IN COMPLEX WITH LIGANDS