Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  TWO CRYSTAL STRUCTURES OF THE CYTOPLASMIC MOLYBDATE-BINDING PROTEIN MODG SUGGEST A NOVEL COOPERATIVE BINDING MECHANISM AND PROVIDE INSIGHTS INTO LIGAND-BINDING SPECIFICITY. PHOSPHATE-GROWN FORM WITH MOLYBDATE AND PHOSPHATE BOUND
 
Authors :  L. Delarbre, C. E. M. Stevenson, D. J. White, L. A. Mitchenall, R. N. Pau, D. M. Lawson
Date :  13 Mar 01  (Deposition) - 11 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Binding Protein, Molybdate Homeostasis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Delarbre, C. E. M. Stevenson, D. J. White, L. A. Mitchenall, R. N. Pau, D. M. Lawson
Two Crystal Structures Of The Cytoplasmic Molybdate-Binding Protein Modg Suggest A Novel Cooperative Binding Mechanism And Provide Insights Into Ligand-Binding Specificity
J. Mol. Biol. V. 308 1063 2001
PubMed-ID: 11352591  |  Reference-DOI: 10.1006/JMBI.2001.4636

(-) Compounds

Molecule 1 - MOLYBDENUM-BINDING-PROTEIN
    Cellular Location: CYTOPLASM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: MODG
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PDJW373
    Expression System Vector Type: PLASMID
    Gene: MODG
    Organism Scientific: AZOTOBACTER VINELANDII
    Organism Taxid: 354
    Plasmid: PDJW373
    Strain: E162
    Synonym: MODG

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MOO2Ligand/IonMOLYBDATE ION
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1MOO6Ligand/IonMOLYBDATE ION
2PO46Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:76 , ALA A:77 , ARG A:78 , LYS A:132 , ALA A:133 , SER A:134 , PO4 A:1146 , HOH A:2036 , HOH A:2037 , HOH A:2076 , HOH A:2077BINDING SITE FOR RESIDUE PO4 A1145
2AC2SOFTWAREASN A:22 , VAL A:38 , VAL A:39 , THR A:40 , LYS A:132 , SER A:134 , PO4 A:1145BINDING SITE FOR RESIDUE PO4 A1146
3AC3SOFTWAREALA A:92 , VAL A:93 , ASN A:94BINDING SITE FOR RESIDUE MOO A1143
4AC4SOFTWARESER A:4 , ALA A:5 , ARG A:6 , LYS A:60 , ALA A:61 , PRO A:62 , THR A:112 , ALA A:115 , HOH A:2075BINDING SITE FOR RESIDUE MOO A1144

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H9J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H9J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H9J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H9J)

(-) Exons   (0, 0)

(no "Exon" information available for 1H9J)

(-) Sequences/Alignments

Asymmetric 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:145
 aligned with Q44529_AZOVI | Q44529 from UniProtKB/TrEMBL  Length:142

    Alignment length:145
                               1                                                                                                                                             
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137     
         Q44529_AZOVI     - ---MKISARNVFKGTVSALKEGAVNAEVDILLGGGDKLAAVVTLESARSLQLAAGKEVVAVVKAPWVLLMTDSSGYRLSARNILTGTVKTIETGAVNAEVTLALQGGTEITSMVTKEAVAELGLKPGASASAVIKASNVILGVPA 142
               SCOP domains d1h9ja1 A:-3-73 Cytoplasmic molybdate-binding protein ModG                  d1h9ja2 A:74-142 Cytoplasmic molybdate-binding protein ModG           SCOP domains
               CATH domains ---1h9jA02 A:1-61,A:132-141  [code=2.40.50.100, no name defined]1h9jA01 A:62-131  [code=2.40.50.100, no name defined]                 1h9jA02   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeee...eeeeeeee....eeeeeeehhhhhhh......eeeeeehhhhheee...........eeeeeeeeeeee...eeeeeeee....eeeeeeehhhhhhhh.....eeeeeehhhhheee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h9j A  -3 GSHMKISARNVFKGTVSALKEGAVNAEVDILLGGGDKLAAVVTLESARSLQLAAGKEVVAVVKAPWVLLMTDSSGYRLSARNILTGTVKTIETGAVNAEVTLALQGGTEITSMVTKEAVAELGLKPGASASAVIKASNVILGVPA 142
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137     
                             -1|                                                                                                                                             
                               1
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H9J)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q44529_AZOVI | Q44529)
molecular function
    GO:0030151    molybdenum ion binding    Interacting selectively and non-covalently with molybdenum (Mo) ions.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

 Visualization

(-) Interactive Views

Asymmetric 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
    MOO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1h9j)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1h9j
    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
  Q44529_AZOVI | Q44529
    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
  Q44529_AZOVI | Q44529
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q44529_AZOVI | Q44529: 1h9k 1h9m

(-) Related Entries Specified in the PDB File

1atg AZOTOBACTER VINELANDII PERIPLASMIC MOLYBDATE- BINDING PROTEIN
1h9k TWO CRYSTAL STRUCTURES OF THE CYTOPLASMIC MOLYBDATE-BINDING PROTEIN MODG SUGGEST A NOVEL COOPERATIVE BINDING MECHANISM AND PROVIDE INSIGHTS INTO LIGAND-BINDING SPECIFICITY. PHOSPHATE-GROWN FORM WITH TUNGSTATE AND PHOSPHATE BOUND
1h9m TWO CRYSTAL STRUCTURES OF THE CYTOPLASMIC MOLYBDATE-BINDING PROTEIN MODG SUGGEST A NOVEL COOPERATIVE BINDING MECHANISM AND PROVIDE INSIGHTS INTO LIGAND-BINDING SPECIFICITY. PEG-GROWN FORM WITH MOLYBDATE BOUND