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
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)

(-) Description

Title :  BIPHENYLALANINE MODIFIED THREONYL-TRNA SYNTHETASE FROM PYROCOCCUS ABYSSI: I11BIF, F42W, Y79A, AND F123Y MUTANT
 
Authors :  A. D. Pearson, J. H. Mills, Y. Song, F. Nasertorabi, G. W. Han, D. Baker, R. C. Stevens, P. G. Schultz
Date :  30 Dec 14  (Deposition) - 18 Mar 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Beta-Alpha-Beta Fold, Editing Domain, Trna-Synthetase, Ligase, Biphenylalanine And Unnatural Amino Acid, Threonine-Trna Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Pearson, J. H. Mills, Y. Song, F. Nasertorabi, G. W. Han, D. Baker, R. C. Stevens, P. G. Schultz
Transition States. Trapping A Transition State In A Computationally Designed Protein Bottle.
Science V. 347 863 2015
PubMed-ID: 25700516  |  Reference-DOI: 10.1126/SCIENCE.AAA2424

(-) Compounds

Molecule 1 - THREONINE--TRNA LIGASE
    Chains: A
    EC Number: 6.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B AND PULTRA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: THREONYL-TRNA SYNTHETASE
    Gene: PAB1490, PYRAB13430, THRS
    Mutation: YES
    Organism Scientific: PYROCOCCUS ABYSSI GE5
    Organism Taxid: 272844
    Strain: GE5 / ORSAY
    Synonym: THREONYL-TRNA SYNTHETASE, THRRS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1BIF1Mod. Amino Acid(R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)PROPANOIC ACID
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1BIF2Mod. Amino Acid(R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)PROPANOIC ACID
2PEG6Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:129 , HIS A:130 , PRO A:131 , ALA A:133 , GLU A:134 , HOH A:320BINDING SITE FOR RESIDUE PEG A 201
2AC2SOFTWARETYR A:13 , GLY A:33 , ARG A:34 , PHE A:77 , GLY A:113 , LYS A:114BINDING SITE FOR RESIDUE PEG A 202
3AC3SOFTWARELYS A:21 , ASN A:22 , GLU A:54 , LEU A:58 , ARG A:100 , HOH A:349 , HOH A:363BINDING SITE FOR RESIDUE PEG A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S02)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4S02)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S02)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S02)

(-) Exons   (0, 0)

(no "Exon" information available for 4S02)

(-) 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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee........hhhh.eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhh.eeee....eeeeeeeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4s02 A   1 MRVLLIHADYfEYEVKDKALKNPEPISEDMKRGRMEEVLVAWISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVAPWAELAKPSVAMDILNRVYQGLKERGFNVGKAPFGYYIAYKISCKGHPLAELSRTIVPE 142
                                    10|       20        30        40        50        60        70        80 ||     94       104       114       124       134        
                                     11-BIF                                                                 82|                                                       
                                                                                                             87
   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 4S02)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S02)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S02)

(-) Gene Ontology  (11, 11)

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
    BIF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ 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 4s02)
 
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
  4s02
    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
  SYT_PYRAB | Q9UZ14
    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)
  6.1.1.3
    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
  SYT_PYRAB | Q9UZ14
    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
        SYT_PYRAB | Q9UZ14: 1y2q 2hkz 2hl0 2hl1 2hl2 3pd2 3pd3 3pd4 3pd5 4rrq 4rrr 4s03 4s0i 4s0j 4s0k 4s0l

(-) Related Entries Specified in the PDB File

1y2q PARENT SCAFFOLD