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 BLEOMYCIN-BINDING PROTEIN FROM STREPTOALLOTEICHUS HINDUSTANUS COMPLEXED WITH BLEOMYCIN DERIVATIVE
 
Authors :  H. Okumura, I. Miyazaki, S. Simizu, H. Osada
Date :  06 Feb 08  (Deposition) - 17 Feb 09  (Release) - 17 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibiotic Resistance, Bleomycin, Ligand Binding Protein, Antibiotic Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Miyazaki, H. Okumura, S. Simizu, Y. Takahashi, N. Kanoh, Y. Nonomura, H. Osada
Structure-Affinity Relationship Study Of Bleomycins And Shble Protein Using A Chemical Array
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BLEOMYCIN RESISTANCE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET C
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOALLOTEICHUS HINDUSTANUS
    Organism Taxid: 2017
    Synonym: BLEOMYCIN-BINDING PROTEIN, BRP, PHLEOMYCIN RESISTANCE PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1BY62Ligand/Ion[(2S,3R,4R,5S,6S)-2-[(3R,4R,5R,6R)-2-[(1R,2S)-2-[[6-AMINO-2-[(1S)-3-AMINO-1-[(2,3-DIAMINO-3-OXOPROPYL)AMINO]-3-OXOPROPYL]-5-METHYLPYRIMIDINE-4-CARBONYL]AMINO]-3-[[(2S,3R,4R)-5-[[(2R,3S)-1-[2-[4-[4-[3-[4-(3-AMINOPROPYLAMINO)BUTYLAMINO]PROPYLCARBAMOYL]-1,3-THIAZOL-2-YL]-1,3-THIAZOL-2-YL]ETHYLAMINO]-3-HYDROXY-1-OXOBUTAN-2-YL]AMINO]-3-HYDROXY-4-METHYL-5-OXOPENTAN-2-YL]AMINO]-1-(3H-IMIDAZOL-4-YL)-3-OXOPROPOXY]-4,5-DIHYDROXY-6-(HYDROXYMETHYL)OXAN-3-YL]OXY-3,5-DIHYDROXY-6-(HYDROXYMETHYL)OXAN-4-YL]CARBAMATE
2CL3Ligand/IonCHLORIDE ION
3CU2Ligand/IonCOPPER (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:14 , ASP A:36 , ASP A:37 , ALA A:52 , GLN A:54 , PRO A:59 , ASP A:60 , ASN A:61 , THR A:62 , LEU A:63 , TRP A:65 , PHE A:86 , ARG A:87 , TRP A:102 , ALA A:107 , ARG A:109 , GLY A:113 , CYS A:115 , HIS A:117 , CU A:302 , CL A:303 , HOH A:508 , HOH A:518 , HOH A:520 , HOH A:533 , HOH A:548 , HOH A:549 , HOH A:559 , HOH A:566 , HOH A:569 , HOH A:578 , HOH A:579 , HOH A:595 , HOH A:642 , PHE B:33 , GLU B:35 , PHE B:38 , PHE B:49 , SER B:51 , ALA B:52 , VAL B:53 , HOH B:574 , HOH B:606BINDING SITE FOR RESIDUE BY6 A 301
2AC2SOFTWAREBY6 A:301BINDING SITE FOR RESIDUE CU A 302
3AC3SOFTWARELEU A:63 , HIS A:117 , BY6 A:301BINDING SITE FOR RESIDUE CL A 303
4AC4SOFTWAREPHE A:33 , GLU A:35 , PHE A:38 , ALA A:52 , VAL A:53 , ARG A:87 , HOH A:614 , HOH A:630 , PRO B:59 , ASP B:60 , ASN B:61 , THR B:62 , LEU B:63 , TRP B:65 , ALA B:107 , ARG B:109 , GLY B:113 , CYS B:115 , HIS B:117 , CU B:402 , CL B:403 , HOH B:555 , HOH B:584 , HOH B:638 , HOH B:693 , HOH B:694 , HOH B:695 , HOH B:699BINDING SITE FOR RESIDUE BY6 B 401
5AC5SOFTWAREBY6 B:401 , CL B:403BINDING SITE FOR RESIDUE CU B 402
6AC6SOFTWAREBY6 B:401 , CU B:402BINDING SITE FOR RESIDUE CL B 403
7AC7SOFTWAREALA A:2 , GLU B:21 , ASP B:25 , GLU B:73BINDING SITE FOR RESIDUE CL B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZHP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZHP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VOCPS51819 Vicinal oxygen chelate (VOC) domain profile.BLE_STRHI3-121
 		  2A:3-121
B:3-121

(-) Exons   (0, 0)

(no "Exon" information available for 2ZHP)

(-) 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:120
 aligned with BLE_STRHI | P17493 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
            BLE_STRHI     2 AKLTSAVPVLTARDVAGAVEFWTDRLGFSRDFVEDDFAGVVRDDVTLFISAVQDQVVPDNTLAWVWVRGLDELYAEWSEVVSTNFRDASGPAMTEIGEQPWGREFALRDPAGNCVHFVAE 121
               SCOP domains d2zhpa_ A: automated matches                                                                                             SCOP domains
               CATH domains 2zhpA00 A:2-121 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeee.hhhhhhhhhhhh...eeeee...eeeeee..eeeeeee.....hhhh.eeeeeeehhhhhhhhhhh............ee...eee..eeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -VOC  PDB: A:3-121 UniProt: 3-121                                                                                        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zhp A   2 AKLTSAVPVLTARDVAGAVEFWTDRLGFSRDFVEDDFAGVVRDDVTLFISAVQDQVVPDNTLAWVWVRGLDELYAEWSEVVSTNFRDASGPAMTEIGEQPWGREFALRDPAGNCVHFVAE 121
                                    11        21        31        41        51        61        71        81        91       101       111       121


Chain B from PDB  Type:PROTEIN  Length:111
 aligned with BLE_STRHI | P17493 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
            BLE_STRHI     2 AKLTSAVPVLTARDVAGAVEFWTDRLGFSRDFVEDDFAGVVRDDVTLFISAVQDQVVPDNTLAWVWVRGLDELYAEWSEVVSTNFRDASGPAMTEIGEQPWGREFALRDPAGNCVHFVAE 121
               SCOP domains d2zhpb_ B: automated matches                                                                                             SCOP domains
               CATH domains 2zhpB00 B:2-121 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeee.hhhhhhhhhhhh...eeeee...eeeeee..eeeeeee.....hhhh.eeeeeeehhhhhhhhhh.....-------.ee......--..eeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -VOC  PDB: B:3-121 UniProt: 3-121                                                                                        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zhp B   2 AKLTSAVPVLTARDVAGAVEFWTDRLGFSRDFVEDDFAGVVRDDVTLFISAVQDQVVPDNTLAWVWVRGLDELYAEWSEVVST-------PAMTEIGEQ--GREFALRDPAGNCVHFVAE 121
                                    11        21        31        41        51        61        71        81  |      -|       |- |     111       121
                                                                                                             84      92     100  |                  
                                                                                                                               103
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BLE_STRHI | P17493)
molecular function
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
biological process
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

 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
    BY6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CU  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2zhp)
 

(-) 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
  2zhp
    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
  BLE_STRHI | P17493
    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
  BLE_STRHI | P17493
    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
        BLE_STRHI | P17493: 1byl 1xrk

(-) Related Entries Specified in the PDB File

1byl WILD-TYPE SHBLE
1xrk THERMOSTABLE MUTANT OF SHBLE COMPLEXED WITH BLEOMYCIN A2