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 :  PURPLE ACID PHOSPHATASE FROM RAT BONE
 
Authors :  Y. Lindqvist, E. Johansson, H. Kaija, P. Vihko, G. Schneider
Date :  26 Mar 99  (Deposition) - 15 Sep 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Metal Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Lindqvist, E. Johansson, H. Kaija, P. Vihko, G. Schneider
Three-Dimensional Structure Of A Mammalian Purple Acid Phosphatase At 2. 2 A Resolution With A Mu-(Hydr)Oxo Bridged Di-Iron Center.
J. Mol. Biol. V. 291 135 1999
PubMed-ID: 10438611  |  Reference-DOI: 10.1006/JMBI.1999.2962
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PURPLE ACID PHOSPHATASE)
    CellOSTEOCLAST
    ChainsA
    EC Number3.1.3.2
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System GeneACP5
    Expression System PlasmidPVL1392
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System VectorBACULOVIRUS
    Expression System Vector TypeVIRUS
    GeneACP5
    OrganelleLYSOSOME
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    Other DetailsGLYCOSIDIC LINK BETWEEN ASN 118 AND NAG 344 GLYCOSIDIC LINK BETWEEN NAG 344 AND NAG 345
    SynonymTARTRATE-RESISTANT ACID PHOSPHATASE
    TissueBONE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO42Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
12FEAUTHORASN A:112 , HIS A:242 , HIS A:207 , ASP A:73 , TYR A:76 , ASP A:35 , HIS A:244 , SO4 A:437 , HOH A:588 , HOH A:591 , FE A:433 , FE A:434BINUCLEAR IRON-CENTER
2AC1SOFTWAREALA A:83 , ASN A:118 , ALA A:121 , NAG A:345 , HOH A:584BINDING SITE FOR RESIDUE NAG A 344
3AC2SOFTWARENAG A:344BINDING SITE FOR RESIDUE NAG A 345
4AC3SOFTWAREASP A:35 , ASP A:73 , TYR A:76 , HIS A:244 , FE A:434 , SO4 A:437 , HOH A:588 , HOH A:591BINDING SITE FOR RESIDUE FE A 433
5AC4SOFTWAREASP A:73 , ASN A:112 , HIS A:207 , HIS A:242 , FE A:433 , SO4 A:437 , HOH A:588BINDING SITE FOR RESIDUE FE A 434
6AC5SOFTWAREGLU A:90 , ASP A:94 , HIS A:284 , HOH A:536BINDING SITE FOR RESIDUE ZN A 435
7AC6SOFTWAREHIS A:216 , SO4 A:437 , HOH A:527 , HOH A:590BINDING SITE FOR RESIDUE ZN A 436
8AC7SOFTWAREASP A:73 , ASN A:112 , HIS A:113 , HIS A:216 , HIS A:242 , HIS A:244 , FE A:433 , FE A:434 , ZN A:436 , HOH A:573 , HOH A:588 , HOH A:591BINDING SITE FOR RESIDUE SO4 A 437
9AC8SOFTWAREARG A:184 , SER A:188 , LYS A:191BINDING SITE FOR RESIDUE SO4 A 438

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:42 -Pro A:43
2Tyr A:76 -Phe A:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QHW)

(-) 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:300
 aligned with PPA5_RAT | P29288 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:300
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325
             PPA5_RAT    26 STLRFVAVGDWGGVPNAPFHTAREMANAKEIARTVQIMGADFIMSLGDNFYFTGVHDANDKRFQETFEDVFSDRALRNIPWYVLAGNHDHLGNVSAQIAYSKISKRWNFPSPYYRLRFKVPRSNITVAIFMLDTVMLCGNSDDFVSQQPEMPRDLGVARTQLSWLKKQLAAAKEDYVLVAGHYPIWSIAEHGPTRCLVKNLRPLLAAYGVTAYLCGHDHNLQYLQDENGVGYVLSGAGNFMDPSVRHQRKVPNGYLRFHYGSEDSLGGFTYVEIGSKEMSITYVEASGKSLFKTSLPRRP 325
               SCOP domains d1qhwa_ A: Mammalian purple acid phosphatase                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1qhwA00 A:26-325  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --Metallophos-1qhwA01 A:28-246                                                                                                                                                                                               ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.............hhhhhhhhhhhhhhhhh...eeee...............hhhhh........hhh...eee......hhh..hhhhhhhhh...........eeeeee......eeeeee..hhhhh..hhh...........hhhhhhhhhhhhhhh......eeeee..............hhhhhh.hhhhhhh...eeee.....eeeee.....eeeee............hhh.....eeeee.......eeeeeee...eeeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qhw A  26 STLRFVAVGDWGGVPNAPFHTAREMANAKEIARTVQIMGADFIMSLGDNFYFTGVHDANDKRFQETFEDVFSDRALRNIPWYVLAGNHDHLGNVSAQIAYSKISKRWNFPSPYYRLRFKVPRSNITVAIFMLDTVMLCGNSDDFVSQQPEMPRDLGVARTQLSWLKKQLAAAKEDYVLVAGHYPIWSIAEHGPTRCLVKNLRPLLAAYGVTAYLCGHDHNLQYLQDENGVGYVLSGAGNFMDPSVRHQRKVPNGYLRFHYGSEDSLGGFTYVEIGSKEMSITYVEASGKSLFKTSLPRRP 325
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPA5_RAT | P29288)
molecular function
    GO:0003993    acid phosphatase activity    Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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.
biological process
    GO:0045453    bone resorption    The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0033555    multicellular organismal response to stress    Any process that results in a change in state or activity of a multicellular organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0030316    osteoclast differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0033591    response to L-ascorbic acid    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 L-ascorbic acid (vitamin C) stimulus.
    GO:0070723    response to cholesterol    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 a cholesterol stimulus.
    GO:0014070    response to organic cyclic compound    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 organic cyclic compound stimulus.
    GO:0010043    response to zinc ion    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 a zinc ion stimulus.
cellular component
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

 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
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    2FE  [ RasMol ]  +environment [ RasMol ]
    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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:42 - Pro A:43   [ RasMol ]  
    Tyr A:76 - Phe A:77   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1qhw
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PPA5_RAT | P29288
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.2
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PPA5_RAT | P29288
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PPA5_RAT | P292881qfc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QHW)