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 :  STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.5-8F WITH A BOUND 1,3-DIKETONE INHIBITOR
 
Authors :  R. Obexer, P. R. E. Mittl, D. Hilvert
Date :  04 Sep 15  (Deposition) - 17 Aug 16  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase, Retro-Aldolase, Protein Engineering, Enzyme Design, Directed Evolution (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Obexer, A. Godina, X. Garrabou, P. R. Mittl, D. Baker, A. D. Griffiths, D. Hilvert
Emergence Of A Catalytic Tetrad During Evolution Of A Highl Active Artificial Aldolase.
Nat Chem V. 9 50 2017
PubMed-ID: 27995916  |  Reference-DOI: 10.1038/NCHEM.2596

(-) Compounds

Molecule 1 - RA95.5-8F
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Other Details: THE SEQUENCE WAS DESIGNED BASED ON INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE NATURALLY FOUND IN SULFOLOBUS SOLFATARICUS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1LLK1Ligand/Ion(2E)-1-(6-METHOXYNAPHTHALEN-2-YL)BUT-2-EN-1-ONE
2MHO1Mod. Amino AcidS-OXYMETHIONINE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:1004 , GLN A:1014 , ARG A:1036 , ARG A:1043 , HOH A:2060 , HOH A:2107 , HOH A:2279 , HOH A:2280BINDING SITE FOR RESIDUE PO4 A 4002
2AC2SOFTWAREASP A:1011 , ARG A:1018 , ARG A:1043 , LYS A:1087 , HOH A:2061 , HOH A:2281 , HOH A:2283BINDING SITE FOR RESIDUE PO4 A 4003
3AC3SOFTWARETRP A:1008 , TYR A:1051 , SER A:1056 , PRO A:1057 , LYS A:1083 , PHE A:1089 , ASN A:1110 , MET A:1182 , PHE A:1184 , GLU A:1185 , THR A:1186 , GLY A:1187 , HOH A:2122 , HOH A:2150 , HOH A:2151 , HOH A:2284BINDING SITE FOR RESIDUE LLK A 5001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AN7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AN7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AN7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AN7)

(-) Exons   (0, 0)

(no "Exon" information available for 5AN7)

(-) 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:244
                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.............hhhhhhhhhhhhh...eeeee........hhhhhhhhhh....eeeee........hhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeee..........hhhhhhhhhh......eeeeee.....hhhhhhhhh....eeehhhhhhh.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5an7 A 1002 PRYLKGWLEDVVQLSLRRPSVHASRQRPIISLNERILEFNKRNITAIIAYYLRKSPVERDPIEYAKYMEPYAVGLSIKTEEKYFDGSYEMLRKIASSVSIPILMNDFIVKESQIDDAYNLGADTVLLIVEILTERELESLLEYARGYGMEPLILINDENDLDIALRIGARFITIYSMNFETGEINKENQRKLISMIPSNVVKVPLLDFFEPNEIEELRKLGVNAFMISSSLmRNPEKIKELIEG 1249
                                  1011      1021      1031      1041      1051     |1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235 |    1245    
                                                                                1057|                                                                                                                                                                           1237-MHO        
                                                                                 1062
   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 5AN7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AN7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AN7)

(-) Gene Ontology  (10, 10)

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
    LLK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MHO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5an7)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  5an7
    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
  TRPC_SULSO | Q06121
    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)
  (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
  TRPC_SULSO | Q06121
    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
        TRPC_SULSO | Q06121: 1a53 1igs 1juk 1jul 1lbf 1lbl 2c3z 3nyz 3nz1 3tc6 3tc7 4a29 4a2r 4a2s 4iww 4ix0 4lny 4ou1 5aou 5k7j

(-) Related Entries Specified in the PDB File

5aou STRUCTURE OF THE ENGINEERED RETRO-ALDOLASE RA95.5-8F APO