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

(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE EVOLUTION OF A NON-BIOLOGICAL PROTEIN
 
Authors :  M. Smith, M. Rosenow, M. Wang, J. P. Allen, J. W. Szostak, J. C. Chaput
Date :  28 Feb 07  (Deposition) - 05 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha/Beta Fold, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Smith, M. A. Rosenow, M. Wang, J. P. Allen, J. W. Szostak, J. C. Chaput
Structural Insights Into The Evolution Of A Non-Biological Protein: Importance Of Surface Residues In Protein Fold Optimization.
Plos One V. 2 E467 2007
PubMed-ID: 17520026  |  Reference-DOI: 10.1371/JOURNAL.PONE.0000467

(-) Compounds

Molecule 1 - A NON-BIOLOGICAL ATP BINDING PROTEIN WITH TWO MUTATIONS N32D AND D65V
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL1Ligand/IonCHLORIDE ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL-1Ligand/IonCHLORIDE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:23 , CYS A:26 , CYS A:46 , CYS A:49BINDING SITE FOR RESIDUE ZN A 200
2AC2SOFTWARELYS A:10 , TRP A:67 , LEU A:68BINDING SITE FOR RESIDUE CL A 300
3AC3SOFTWAREASP A:32 , LYS A:34 , ARG A:41 , TYR A:43 , ASN A:44 , MET A:45 , PHE A:50 , HIS A:62 , GLY A:63 , HIS A:64 , HOH A:510 , HOH A:535 , HOH A:542 , HOH A:549 , HOH A:574BINDING SITE FOR RESIDUE ATP A 500
4AC4SOFTWARELEU A:14 , LYS A:15 , TYR A:18 , THR A:48 , CYS A:49 , HOH A:604 , HOH A:605 , HOH A:608 , HOH A:609 , HOH A:610BINDING SITE FOR RESIDUE 1PE A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P09)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P09)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P09)

(-) Exons   (0, 0)

(no "Exon" information available for 2P09)

(-) 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:69
                                                                                                    
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...........eeee..eeeee..hhhhhhhhhhhh......eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                  2p09 A  5 DDDDKKTNWLKRIYRVRPCVKCKVAPRDWKVKNKHLRIYNMCKTCFNNSIDIGDDTYHGHVDWLMYADS 73
                                    14        24        34        44        54        64
   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 2P09)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P09)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2P09)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2P09)

 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ 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
(no "Cis Peptide Bonds" information available for 2p09)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  2p09
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2P09)

(-) Related Entries Specified in the PDB File

2p05