Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TRUNCATED ACYLPHOSPHATASE FROM S. SULFATARICUS
 
Authors :  I. Dilovic, M. Bolognesi, S. Ricagno
Date :  20 Jan 14  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Native-Like Aggregation, Hydrolase, Acylphosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Dilovic, M. Bolognesi, S. Ricagno
Crystal Structure Of Truncated Acylphosphatase From S. Sulfataricus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACYLPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: DELTA-11 ACP
    Gene: ACYP, SSO0887
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 273057
    Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
    Synonym: ACYLPHOSPHATE PHOSPHOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:17BINDING SITE FOR RESIDUE CL A 201
2AC2SOFTWAREGLY A:28 , PHE A:29 , ARG A:30BINDING SITE FOR RESIDUE CL A 202
3AC3SOFTWARETYR A:91BINDING SITE FOR RESIDUE CL A 203
4AC4SOFTWAREARG A:19 , TYR A:21 , ALA A:78 , ASP A:85BINDING SITE FOR RESIDUE NA A 204
5AC5SOFTWAREASP B:97 , PHE B:98BINDING SITE FOR RESIDUE CL B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OJ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OJ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4OJ1)

(-) 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:90
                                                                                                                          
               SCOP domains d4oj1a_ A: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeee....hhhhhhhhhhhhhh.eeeeee.....eeeeeeeehhhhhhhhhhhh......eeeeeeeeeee.......eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4oj1 A  12 MLKRMYARVYGLVQGVGFRKFVQIHAIRLGIKGYAKNLPDGSVEVVAEGYEEALSKLLERIKQGPPAAEVEKVDYSFSEYKGEFEDFETY 101
                                    21        31        41        51        61        71        81        91       101


Chain B from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains d4oj1b_ B: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeee....hhhhhhhhhhhhhh.eeeeee.....eeeeeeeehhhhhhhhhhhhhh....eeeeeeeeee........eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4oj1 B  12 MLKRMYARVYGLVQGVGFRKFVQIHAIRLGIKGYAKNLPDGSVEVVAEGYEEALSKLLERIKQGPPAAEVEKVDYSFSEYKGEFEDFETY 101
                                    21        31        41        51        61        71        81        91       101
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OJ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OJ1)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4oj1)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  4oj1
    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
  ACYP_SULSO | Q97ZL0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.1.7
    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
  ACYP_SULSO | Q97ZL0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ACYP_SULSO | Q97ZL0: 1y9o 2bjd 2bje 4oix 4oj3 4ojg 4ojh

(-) Related Entries Specified in the PDB File

4oix 4oj3 4ojg 4ojh