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 CALCIUM-LOADED S100B BOUND TO SBI4434
 
Authors :  M. C. Cavalier, P. D. Pierce, P. T. Wilder, D. Neau, E. A. Toth, D. J. Weber
Date :  22 Apr 14  (Deposition) - 05 Nov 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.08
Chains :  Asym./Biol. Unit :  A,X
Keywords :  Malignant Melanoma, Calcium Binding, Covalent Inhibitor, Complex, Metal Binding Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. Cavalier, A. D. Pierce, P. T. Wilder, M. J. Alasady, K. G. Hartman, D. B. Neau, T. L. Foley, A. Jadhav, D. J. Maloney, A. Simeonov, E. A. Toth D. J. Weber
Covalent Small Molecule Inhibitors Of Ca(2+)-Bound S100B.
Biochemistry V. 53 6628 2014
PubMed-ID: 25268459  |  Reference-DOI: 10.1021/BI5005552

(-) Compounds

Molecule 1 - PROTEIN S100-B
    ChainsX, A
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneS100B
    Organism CommonBOVINE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymS-100 PROTEIN BETA CHAIN,S-100 PROTEIN SUBUNIT BETA,S100 CALCIUM-BINDING PROTEIN B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2NQS2Ligand/Ion2-[(2-HYDROXYETHYL)SULFANYL]NAPHTHALENE-1,4-DIONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE X:43 , LEU X:44 , ALA X:83 , CYS X:84 , PHE X:88 , HOH X:221 , HOH X:339binding site for residue NQS X 101
2AC2SOFTWARESER X:18 , GLU X:21 , ASP X:23 , LYS X:26 , GLU X:31 , HOH X:280binding site for residue CA X 102
3AC3SOFTWAREASP X:61 , ASP X:63 , ASP X:65 , GLU X:67 , GLU X:72 , HOH X:288binding site for residue CA X 103
4AC4SOFTWARESER A:18 , GLU A:21 , ASP A:23 , LYS A:26 , GLU A:31 , HOH A:291binding site for residue CA A 102
5AC5SOFTWAREASP A:61 , ASP A:63 , ASP A:65 , GLU A:67 , GLU A:72 , HOH A:294 , HOH A:357binding site for residue CA A 103
6AC6SOFTWAREPHE A:43 , ILE A:80 , THR A:81 , THR A:82 , ALA A:83 , HIS A:85 , GLU A:86 , PHE A:87 , PHE A:88 , HOH A:338binding site for Di-peptide NQS A 101 and CYS A 84

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PE0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PE0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PE0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PE0)

(-) Exons   (0, 0)

(no "Exon" information available for 4PE0)

(-) 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:92
                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  4pe0 A  0 MSELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFFEHE 91
                                     9        19        29        39        49        59        69        79        89  

Chain X from PDB  Type:PROTEIN  Length:89
                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  4pe0 X  0 MSELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFF 88
                                     9        19        29        39        49        59        69        79         

   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 4PE0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PE0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PE0)

(-) Gene Ontology  (28, 28)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NQS  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4pe0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4pe0
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  S100B_BOVIN | P02638
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  S100B_BOVIN | P02638
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        S100B_BOVIN | P026381cfp 1mho 1psb 3cr2 3cr4 3cr5 3gk1 3gk2 3gk4 3iqo 3iqq 3lk0 3lk1 3lle 3rlz 3rm1 4fqo 4pdz 4pe1 4pe4 4pe7 5dkn 5dkq 5dkr 5er4 5er5

(-) Related Entries Specified in the PDB File

4pdz 4pe1 4pe4 4pe7