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 THE NEOCARZINOSTATIN 3TES24 MUTANT BOUND TO TESTOSTERONE HEMISUCCINATE.
 
Authors :  A. Drevelle, M. Graille, B. Heyd, I. Sorel, N. Ulryck, F. Pecorari, M. Desmadril, H. Van Tilbeurgh, P. Minard
Date :  06 Jan 06  (Deposition) - 22 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Antibiotic, Phage-Display, Hapten Binding, Neocarzinostatin, Antimicrobial, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Drevelle, M. Graille, B. Heyd, I. Sorel, N. Ulryck, F. Pecorari, M. Desmadril, H. Van Tilbeurgh, P. Minard
Structures Of In Vitro Evolved Binding Sites On Neocarzinostatin Scaffold Reveal Unanticipated Evolutionary Pathways.
J. Mol. Biol. V. 358 455 2006
PubMed-ID: 16529771  |  Reference-DOI: 10.1016/J.JMB.2006.02.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEOCARZINOSTATIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BLR(DE3)PLYSS
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: STREPTOMYCES CARZINOSTATICUS
    Organism Taxid: 1897
    Synonym: NCS, MITOMALCIN, MMC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2TH22Ligand/IonTESTOSTERONE HEMISUCCINATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:14 , ASP A:15 , ARG A:71 , HOH A:2113 , HOH A:2114 , HOH A:2115BINDING SITE FOR RESIDUE SO4 A 117
2AC2SOFTWARETHR A:8 , LYS A:20 , TRP A:33 , ALA A:35 , TYR A:47 , ASN A:52 , PHE A:78 , ARG A:82 , SER A:98 , ALA A:100 , ALA A:101 , GLY A:102 , TH2 A:121 , HOH A:2012 , HOH A:2013 , HOH A:2116BINDING SITE FOR RESIDUE TH2 A 120
3AC3SOFTWARETRP A:37 , TRP A:45 , PHE A:78 , ARG A:82 , GLN A:94 , SER A:98 , GLU A:106 , GLY A:107 , HIS A:114 , HIS A:115 , TH2 A:120BINDING SITE FOR RESIDUE TH2 A 121

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:88 -A:93

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:8 -Pro A:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CBO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CBO)

(-) Exons   (0, 0)

(no "Exon" information available for 2CBO)

(-) 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:115
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:115
                                                                                                                                          147  
                                    44        54        64        74        84        94       104       114       124       134       144  |  
           NCZS_STRCZ    35 AAPTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFN--   -
               SCOP domains d2cboa_ A: automated matches                                                                                        SCOP domains
               CATH domains 2cboA00 A:1-115  [code=2.60.40.230, no name defined]                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeeeee......eeeeeeeeeee..eeee.hhhheeee......eeeeee...eeeee.....eeeeee....eeeeeee.........ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2cbo A   1 AAPTATVTPSSGLSDGTVVKVAGAGLQAGTAYWVAQWARVDTGVWAYNPADNSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISFNHH 115
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CBO)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NCZS_STRCZ | P0A3R9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:8 - Pro A:9   [ 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
  2cbo
    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
  NCZS_STRCZ | P0A3R9
    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
  NCZS_STRCZ | P0A3R9
    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
        NCZS_STRCZ | P0A3R9: 1j5h 1j5i 1nco 1noa 1o5p 2cbm 2cbq 2cbt 2g0k 2g0l

(-) Related Entries Specified in the PDB File

1j5h SOLUTION STRUCTURE OF APO-NEOCARZINOSTATIN
1j5i SOLUTION STRUCTURE OF A NOVEL CHROMOPROTEIN DERIVED FROMAPO-NEOCARZINOSTATIN AND A SYNTHETIC CHROMOPHORE
1nco HOLO-NEOCARZINOSTATIN (CONTAINING CHROMOPHORE) COMPLEX WITH APO-CARZINOSTATIN (CONTAINING MPD)
1noa NEOCARZINOSTATIN
1o5p SOLUTION STRUCTURE OF HOLO-NEOCARZINOSTATIN
2cbm CRYSTAL STRUCTURE OF THE APO-FORM OF A NEOCARZINOSTATIN MUTANT EVOLVED TO BIND TESTOSTERONE.
2cbq CRYSTAL STRUCTURE OF THE NEOCARZINOSTATIN 1TES15 MUTANT BOUND TO TESTOSTERONE HEMISUCCINATE.
2cbt CRYSTAL STRUCTURE OF THE NEOCARZINOSTATIN 4TES1 MUTANT BOUND TESTOSTERONE HEMISUCCINATE.