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 :  1.1 ANGSTROM CRYSTAL STRUCTURE OF PUTATIVE MODULATOR OF DRUG ACTIVITY (MDAB) FROM YERSINIA PESTIS CO92.
 
Authors :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papa W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  26 Apr 11  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Flavodoxin-Like Fold, Nadph Dehydrogenase (Quinone) Activity, Flavin Adenine Dinucleotide Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 1 Angstrom Crystal Structure Of Putative Modulator Of Dru Activity (Mdab) From Yersinia Pestis Co92.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MODULATOR OF DRUG ACTIVITY B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: KRX
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MDA66, MDAB, MDAB3, Y3509, YPO0670, YP_2985
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Strain: CO92
    Synonym: MDAB

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:13 , HIS A:15 , SER A:16 , LYS A:17 , GLY A:18 , ALA A:19 , LEU A:20 , ASN A:21 , THR A:23 , PRO A:68 , ALA A:69 , TRP A:70 , TRP A:71 , MET A:72 , THR A:124 , TRP A:125 , ASN A:126 , ALA A:127 , VAL A:171 , PRO A:175 , ILE A:177 , HOH A:197 , HOH A:209 , HOH A:225 , HOH A:228 , HOH A:231 , HOH A:232 , HOH A:233 , HOH A:234 , HOH A:235 , HOH A:260 , HOH A:463 , THR B:87 , TYR B:108BINDING SITE FOR RESIDUE FAD A 195
2AC2SOFTWAREVAL A:27 , ASP A:30 , ILE A:181 , HOH A:234 , HOH A:301BINDING SITE FOR RESIDUE PEG A 196
3AC3SOFTWARETYR A:-5 , THR A:87 , TYR A:108 , PHE B:13 , HIS B:15 , SER B:16 , LYS B:17 , GLY B:18 , ALA B:19 , LEU B:20 , ASN B:21 , THR B:23 , PRO B:68 , ALA B:69 , TRP B:70 , TRP B:71 , MET B:72 , THR B:124 , TRP B:125 , ASN B:126 , ALA B:127 , VAL B:171 , PRO B:175 , ILE B:177 , HOH B:223 , HOH B:241 , HOH B:243 , HOH B:274 , HOH B:340 , HOH B:348 , HOH B:404BINDING SITE FOR RESIDUE FAD B 195

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RPE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RPE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RPE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RPE)

(-) Exons   (0, 0)

(no "Exon" information available for 3RPE)

(-) 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:197
 aligned with Q7CGH8_YERPE | Q7CGH8 from UniProtKB/TrEMBL  Length:194

    Alignment length:197
                               1                                                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       
         Q7CGH8_YERPE     - ---MSNVLIINAMKEFAHSKGALNLTLTNVAADFLRESGHQVKITTVDQGYDIESEIENYLWADTIIYQMPAWWMGEPWILKKYIDEVFTDGHGRLYQSDGRTRSDATKGYGSGGLIQGKTYMLSVTWNAPREAFTDPEQFFHGVGVDGVYLPFHKANQFLGMKPLPTFMCNDVIKQPDIEGDIARYRQHLAENVNS 194
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.........hhhhhhhhhhhhhhhhhh...eeeee.hhh.hhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhh............................eeeeeee....hhhhhh.......hhhhhhhhhhhhhhhhh..ee...eee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rpe A  -5 YFAMSNVLIINAMKEFAHSKGALNLTLTNVAADFLRESGHQVKITTVDQGYDIESEIENYLWADTIIYQMPAWWMGEPWILKKYIDEVFTDGHGRLYQSDGRTRSDATKGYGSGGLIQGKTYMLSVTWNAPREAFTDPEQFFHGVGVDGVYLPFHKANQFLGMKPLPTFMCNDVIKQPDIEGDIARYRQHLAENVNS 194
                             ||      7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       
                             ||                                                                                                                                                                                                  
                            -4|                                                                                                                                                                                                  
                              0                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with Q7CGH8_YERPE | Q7CGH8 from UniProtKB/TrEMBL  Length:194

    Alignment length:195
                             1                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     
         Q7CGH8_YERPE     - -MSNVLIINAMKEFAHSKGALNLTLTNVAADFLRESGHQVKITTVDQGYDIESEIENYLWADTIIYQMPAWWMGEPWILKKYIDEVFTDGHGRLYQSDGRTRSDATKGYGSGGLIQGKTYMLSVTWNAPREAFTDPEQFFHGVGVDGVYLPFHKANQFLGMKPLPTFMCNDVIKQPDIEGDIARYRQHLAENVNS 194
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Flavodoxin_2-3rpeB01 B:2-192                                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) --Flavodoxin_2-3rpeB02 B:2-192                                                                                                                                                                   -- Pfam domains (2)
         Sec.struct. author ....eeeee.........hhhhhhhhhhhhhhhhhh...eeeee.hhh.hhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhh............................eeeeeee....hhhhhh.......hhhhhhhhhhhhhhhhh..ee...eee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rpe B   0 AMSNVLIINAMKEFAHSKGALNLTLTNVAADFLRESGHQVKITTVDQGYDIESEIENYLWADTIIYQMPAWWMGEPWILKKYIDEVFTDGHGRLYQSDGRTRSDATKGYGSGGLIQGKTYMLSVTWNAPREAFTDPEQFFHGVGVDGVYLPFHKANQFLGMKPLPTFMCNDVIKQPDIEGDIARYRQHLAENVNS 194
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189
   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 3RPE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RPE)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Flavoprotein (71)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3RPE)

 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
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rpe)
 

(-) 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
  3rpe
    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
  Q7CGH8_YERPE | Q7CGH8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q7CGH8_YERPE | Q7CGH8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q7CGH8_YERPE | Q7CGH8: 4s24

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3RPE)