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

(-) Description

Title :  CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA
 
Authors :  R. S. Brown, J. C. Dewan, A. Klug
Date :  22 Aug 86  (Deposition) - 24 Oct 86  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  T-Rna, Single Strand, Loops (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Brown, J. C. Dewan, A. Klug
Crystallographic And Biochemical Investigation Of The Lead(Ii)-Catalyzed Hydrolysis Of Yeast Phenylalanine Trna.
Biochemistry V. 24 4785 1985
PubMed-ID: 3907691  |  Reference-DOI: 10.1021/BI00339A012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNAPHE
    Chains: A
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (14, 23)

Asymmetric/Biological Unit (14, 23)
No.NameCountTypeFull Name
11MA1Mod. Nucleotide6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
22MG1Mod. Nucleotide2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
35MC2Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
45MU1Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
57MG1Mod. Nucleotide7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
6H2U2Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
7M2G1Mod. NucleotideN2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
8MG5Ligand/IonMAGNESIUM ION
9OMC1Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
10OMG1Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
11PB3Ligand/IonLEAD (II) ION
12PSU2Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
13SPM1Ligand/IonSPERMINE
14YG1Mod. ResidueWYBUTOSINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA A:9 , G A:22 , A A:23 , G A:24 , C A:25 , G A:45 , 7MG A:46 , PB A:84 , HOH A:162 , HOH A:181 , HOH A:182 , HOH A:190BINDING SITE FOR RESIDUE SPM A 77
2AC2SOFTWAREU A:12 , HOH A:93 , HOH A:150 , HOH A:175BINDING SITE FOR RESIDUE MG A 78
3AC3SOFTWAREG A:20 , A A:21 , HOH A:106BINDING SITE FOR RESIDUE MG A 79
4AC4SOFTWAREG A:19 , G A:20 , U A:59 , PB A:83BINDING SITE FOR RESIDUE MG A 80
5AC5SOFTWAREG A:19 , U A:59 , C A:60 , MG A:80BINDING SITE FOR RESIDUE PB A 83
6AC6SOFTWAREG A:45 , SPM A:77 , HOH A:181 , HOH A:182 , HOH A:190BINDING SITE FOR RESIDUE PB A 84
7AC7SOFTWAREOMC A:32 , U A:33 , A A:36 , YG A:37BINDING SITE FOR RESIDUE PB A 85

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TN2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TN2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TN2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TN2)

(-) Exons   (0, 0)

(no "Exon" information available for 1TN2)

(-) 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:RNA  Length:76
                                                                                                           
                  1tn2 A  1 GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAGgUCcUGUGuuCGaUCCACAGAAUUCGCACCA 76
                                    10     || 20     |  30 | |  | 40     |  50   ||  |60        70      
                                    10-2MG ||       26-M2G | |  | ||     |  |    55-PSU                 
                                          16-H2U          32-OMC| ||     |  |    |  58-1MA              
                                           17-H2U           34-OMG||     |  |    |                      
                                                               37-YG     |  |    |                      
                                                                 39-PSU  |  |    |                      
                                                                  40-5MC |  |    |                      
                                                                        46-7MG   |                      
                                                                           49-5MC|                      
                                                                                54-5MU
   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 1TN2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TN2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TN2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1TN2)

 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
    1MA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    2MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    5MC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    5MU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    7MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    H2U  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    M2G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OMC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OMG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PSU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SPM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    YG  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tn2)
 

(-) 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)
Midas
  spacefill, water
[ mono GIF format | stereo GIF format ]
Setor
  ribbon, sticks
[ mono GIF format | stereo GIF format ]
  ribbon, sticks, labeling
[ mono GIF format | stereo GIF format ]
  spacefill
[ mono GIF format | stereo GIF format ]
  ribbon, spermine, magnesium, lead
[ mono GIF format | stereo GIF format ]
Distance Plot
  representative atom O3*
[ mono GIF format | mono PDF format ]

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1tn2
    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 | HSSP
    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 1TN2)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1TN2)