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 :  CRYSTAL STRUCTURE OF RPA70N IN COMPLEX WITH 5-(4-((4-(5-CARBOXYFURAN-2-YL)PHENYLTHIOAMIDO)METHYL)PHENYL)-1-(3,4-DICHLOROPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC ACID
 
Authors :  M. D. Feldkamp, A. G. Waterson, J. P. Kennedy, J. D. Patrone, N. F. Pelz, A B. Vangamudi, E. M. Sousa-Fagundes, O. W. Rossanese, S. W. Fesik, W. J.
Date :  19 Aug 14  (Deposition) - 19 Nov 14  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
Chains :  Asym./Biol. Unit :  A
Keywords :  Ob-Fold, Protein-Protein Interaction, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Waterson, J. P. Kennedy, J. D. Patrone, N. F. Pelz, M. D. Feldkamp, A. O. Frank, B. Vangamudi, E. M. Souza-Fagundes, O. W. Rossanese, W. J. Chazin, S. W. Fesik
Diphenylpyrazoles As Replication Protein A Inhibitors.
Acs Med Chem Lett V. 6 140 2015
PubMed-ID: 25699140  |  Reference-DOI: 10.1021/ML5003629

(-) Compounds

Molecule 1 - REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN (UNP RESIDUES 1-120)
    Gene: RPA1, REPA1, RPA70
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RP-A P70, REPLICATION FACTOR A PROTEIN 1, RF-A PROTEIN 1, SINGLE-STRANDED DNA-BINDING PROTEIN, REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT, N-TERMINALLY PROCESSED

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
13J01Ligand/Ion5-{4-[({[4-(5-CARBOXYFURAN-2-YL)PHENYL]CARBONOTHIOYL}AMINO)METHYL]PHENYL}-1-(3,4-DICHLOROPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:33 , THR A:34 , ARG A:41 , ARG A:43 , SER A:55 , ALA A:59 , THR A:60 , ASN A:85 , LEU A:87 , ARG A:91 , ILE A:95 , MET A:97 , HOH A:312 , HOH A:326 , HOH A:355 , HOH A:384 , HOH A:392 , HOH A:416BINDING SITE FOR RESIDUE 3J0 A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R4T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R4T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R4T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R4T)

(-) Exons   (0, 0)

(no "Exon" information available for 4R4T)

(-) 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:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..hhhhhhhh........eeeeeeeee.........eeeeee...eeeeeeee...hhhhhhh.......eeeeeeeeeee.....eeeeeeeeeeeehhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r4t A  -1 SHMVGQLSRGAIAAIMQKGDTNIKPILQVINIRPITTGNSPPRYRLLMSDGLNTLSSFMLATQLNPLVEEEQLSSNCVCQIHRFIVNTLKDGRRVVILMELEVLKSAEAVGVKIGNPVPYNE 120
                                     8        18        28        38        48        58        68        78        88        98       108       118
   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 4R4T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R4T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R4T)

(-) Gene Ontology  (38, 38)

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
    3J0  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4r4t)
 

(-) 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
  4r4t
    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
  RFA1_HUMAN | P27694
    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
  RFA1_HUMAN | P27694
    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
        RFA1_HUMAN | P27694: 1ewi 1fgu 1jmc 1l1o 2b29 2b3g 4ijh 4ijl 4ipc 4ipd 4ipg 4iph 4luo 4luv 4luz 4lw1 4lwc 4nb3 4o0a 4r4c 4r4i 4r4o 4r4q 5e7n 5eay 5n85 5n8a

(-) Related Entries Specified in the PDB File

4r4c 4r4i 4r4o 4r4q