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 LP1NTPDASE FROM LEGIONELLA PNEUMOPHILA IN COMPLEX WITH AMPPNP
 
Authors :  H. Ge, J. P. Vivian, T. Beddoe, J. Rossjohn
Date :  24 Nov 09  (Deposition) - 09 Feb 10  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Adenosine Triphosphatase, Ntpdase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Vivian, P. Riedmaier, H. Ge, J. Le Nours, F. M. Sansom, M. C. J. Wilce, E. Byres, M. Dias, J. W. Schmidberger, P. J. Cowan, A. J. F. D'Apice, E. L. Hartland, J. Rossjohn, T. Beddoe
Crystal Structure Of A Legionella Pneumophila Ecto -Triphosphate Diphosphohydrolase, A Structural And Functional Homolog Of The Eukaryotic Ntpdases
Structure V. 18 228 2010
PubMed-ID: 20159467  |  Reference-DOI: 10.1016/J.STR.2009.11.014

(-) Compounds

Molecule 1 - ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 41-393
    Gene: LPG1905
    Organism Scientific: LEGIONELLA PNEUMOPHILA
    Organism Taxid: 272624
    Strain: PHILADELPHIA 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:52 , THR A:53 , MET A:187 , GLY A:189 , GLN A:231 , THR A:232 , GLY A:299 , ASN A:302 , LEU A:303 , TYR A:346 , TYR A:350 , LEU A:353 , HOH A:494 , HOH A:581 , HOH A:589 , HOH A:590 , HOH A:745 , HOH A:750 , HOH A:797 , HOH A:837 , HOH A:842BINDING SITE FOR RESIDUE ANP A 1

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:244 -A:264
2A:330 -A:351

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:82 -Pro A:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AAR)

(-) 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:352
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:352
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391  
         Q5ZUA2_LEGPH    42 HSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA 393
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh......eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhh..........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...eeeeeehhhhhhh.........eeehhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh.........eeee.hhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aar A  42 HSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA 393
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
   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 3AAR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AAR)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5ZUA2_LEGPH | Q5ZUA2)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 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
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:82 - Pro A:83   [ 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
  3aar
    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
  Q5ZUA2_LEGPH | Q5ZUA2
    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
  Q5ZUA2_LEGPH | Q5ZUA2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5ZUA2_LEGPH | Q5ZUA2: 3aap 3aaq 4br4 4br7 4br9 4bra 4brc 4brd 4bre 4brf 4brg 4brh 4bri 4brk 4brl 4brm 4brn 4bro 4brp 4brq 4bvo 4bvp

(-) Related Entries Specified in the PDB File

3aap APO-STRUCTURE
3aaq IN COMPLEX WITH THE INHIBITOR ARL 67156