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 :  HUMAN BRAIN ASPARTOACYLASE MUTANT F295S COMPLEX WITH INTERMEDIATE ANALOG (N-PHOSPHONOMETHYL-L-ASPARTATE)
 
Authors :  Y. S. Wijayasinghe, A. G. Pavlovsky, R. E. Viola
Date :  17 Sep 13  (Deposition) - 30 Jul 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Canavan Disease, N-Acetyl-L-Aspartate, Zinc-Dependent Hydrolase, Aspartoacylase Family, Aminoacylase-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. S. Wijayasinghe, A. G. Pavlovsky, R. E. Viola
Aspartoacylase Catalytic Deficiency As The Cause Of Canavan Disease: A Structural Perspective.
Biochemistry V. 53 4970 2014
PubMed-ID: 25003821  |  Reference-DOI: 10.1021/BI500719K

(-) Compounds

Molecule 1 - ASPARTOACYLASE
    ChainsA, B
    EC Number3.5.1.15
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System CommonPICHIA PASTORIS
    Expression System PlasmidPPICZA
    Expression System StrainKM71H
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    GeneACY2, ASP, ASPA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAMINOACYLASE-2, ACY-2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1AS92Ligand/IonN-[HYDROXY(METHYL)PHOSPHORYL]-L-ASPARTIC ACID
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:21 , GLU A:24 , HIS A:116 , AS9 A:402BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS A:21 , GLU A:24 , ARG A:63 , ASN A:70 , ARG A:71 , HIS A:116 , ASN A:117 , TYR A:164 , ARG A:168 , GLU A:178 , GLU A:285 , TYR A:288 , ZN A:401BINDING SITE FOR RESIDUE AS9 A 402
3AC3SOFTWAREHIS B:21 , GLU B:24 , HIS B:116 , AS9 B:402BINDING SITE FOR RESIDUE ZN B 401
4AC4SOFTWAREHIS B:21 , GLU B:24 , ARG B:63 , ASN B:70 , ARG B:71 , HIS B:116 , ASN B:117 , ILE B:127 , TYR B:164 , ARG B:168 , GLU B:178 , GLU B:285 , TYR B:288 , ZN B:401BINDING SITE FOR RESIDUE AS9 B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MRI)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gly A:101 -Pro A:102
2Ala A:148 -Pro A:149
3Gly A:180 -Pro A:181
4Gly B:101 -Pro B:102
5Ala B:148 -Pro B:149
6Gly B:180 -Pro B:181
7Asp B:266 -Gly B:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MRI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MRI)

(-) Exons   (0, 0)

(no "Exon" information available for 4MRI)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhh......eeeee.hhhhhhh.......hhhhh.hhhhhh.......hhhhhhhhhhhhhhh.........eeeeeee.....eeeeee....hhhhhhhhhhhhhhhh...eeeee.........hhhhhh.eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee...........eee................eeeee....eee.......eee...hhhhh.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mri A  10 HIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEASAKTTKLTLNAKSIRCC 311
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309  

Chain B from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhh.......hhhhh.hhhhhh.......hhhhhhhhhhhhhhh.........eeeeeee.....eeeeee....hhhhhhhhhhhhhhhh...eeeee.........hhhhhh.eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeee............ee................eeee.....eee.......eee...hhhhh.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mri B   9 EHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTSNMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEASAKTTKLTLNAKSIRCC 311
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308   

   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 4MRI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MRI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MRI)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    AS9  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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
    Ala A:148 - Pro A:149   [ RasMol ]  
    Ala B:148 - Pro B:149   [ RasMol ]  
    Asp B:266 - Gly B:267   [ RasMol ]  
    Gly A:101 - Pro A:102   [ RasMol ]  
    Gly A:180 - Pro A:181   [ RasMol ]  
    Gly B:101 - Pro B:102   [ RasMol ]  
    Gly B:180 - Pro B:181   [ 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
  4mri
    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
  ACY2_HUMAN | P45381
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.1.15
    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
  ACY2_HUMAN | P45381
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ACY2_HUMAN | P453812i3c 2o4h 2o53 2q51 4mxu 4nfr 4tnu

(-) Related Entries Specified in the PDB File

2o4h 2o53