Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  HUMAN ACYLPHOSPHATASE(ACPH) SURFACE CHARGE-OPTIMIZED
 
Authors :  A. V. Gribenko, M. M. Patel, J. Liu, S. A. Mccallum, C. Wang, G. I. Makhatadze
Date :  12 Aug 08  (Deposition) - 17 Feb 09  (Release) - 10 Mar 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Protein, Acetylation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. V. Gribenko, M. M. Patel, J. Liu, S. A. Mccallum, C. Wang, G. I. Makhatadze
Rational Stabilization Of Enzymes By Computational Redesign Of Surface Charge-Charge Interactions
Proc. Natl. Acad. Sci. Usa V. 106 2601 2009
PubMed-ID: 19196981  |  Reference-DOI: 10.1073/PNAS.0808220106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACYLPHOSPHATASE-1
    ChainsA
    EC Number3.6.1.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3) PLYSE
    Expression System Taxid562
    Expression System VectorPGIA
    GeneACYP1, ACYPE
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymACYLPHOSPHATE PHOSPHOHYDROLASE 1, ACYLPHOSPHATASE, ORGAN-COMMON TYPE ISOZYME, ACYLPHOSPHATASE, ERYTHROCYTE ISOZYME

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2K7J)

(-) Sites  (0, 0)

(no "Site" information available for 2K7J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K7J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K7J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K7J)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACYLPHOSPHATASE_3PS51160 Acylphosphatase-like domain profile.ACYP1_HUMAN9-99  1A:9-99
2ACYLPHOSPHATASE_1PS00150 Acylphosphatase signature 1.ACYP1_HUMAN14-24  1A:14-24
3ACYLPHOSPHATASE_2PS00151 Acylphosphatase signature 2.ACYP1_HUMAN38-54  1A:38-54

(-) Exons   (0, 0)

(no "Exon" information available for 2K7J)

(-) Sequences/Alignments

NMR Structure
   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:99
 aligned with ACYP1_HUMAN | P07311 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
           ACYP1_HUMAN    1 MAEGNTLISVDYEIFGKVQGVFFRKHTQAEGKKLGLVGWVQNTDRGTVQGQLQGPISKVRHMQEWLETRGSPKSHIDKANFNNEKVILKLDYSDFQIVK 99
               SCOP domains d2k7ja_ A: automated matches                                                                        SCOP domains
               CATH domains 2k7jA00 A:1-99  [code=3.30.70.100, no name defined]                                                 CATH domains
               Pfam domains -Acylphosphatase-2k7jA01 A:2-98                                                                   - Pfam domains
         Sec.struct. author ......eeeeeeee........hhhhhhhhhhhhh..eee.......eeeeeeeehhhhhhhhhhhhh..........................eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------ACYLPHOSPHATASE_3  PDB: A:9-99 UniProt: 9-99                                                PROSITE (1)
                PROSITE (2) -------------ACYLPHOSPHA-------------ACYLPHOSPHATASE_2--------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2k7j A  1 GAEGNTLISVDYEIFGKVQGVFFRKHTQAEGKKLGLVGWVQNTDRGTVQGKLQGPISKVREMQKWLETRGSPESHIDKANFKNEKVILKLDYSDFQIVK 99
                                    10        20        30        40        50        60        70        80        90         

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (ACYP1_HUMAN | P07311)
molecular function
    GO:0003998    acylphosphatase activity    Catalysis of the reaction: an acyl phosphate + H2O = a carboxylate + phosphate.
    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.
biological process
    GO:0006796    phosphate-containing compound metabolic process    The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

 Visualization

(-) Interactive Views

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 2k7j)
 
  Sites
(no "Sites" information available for 2k7j)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2k7j)
 

(-) 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
  2k7j
    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
  ACYP1_HUMAN | P07311
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.1.7
    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
  ACYP1_HUMAN | P07311
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ACYP1_HUMAN | P073112k7k 2vh7 2w4c 2w4p 3toq

(-) Related Entries Specified in the PDB File

2k7k