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 :  N-TERMINAL EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM AEROPYRUM PERNIX WITH L-THR3AA (SNAPSHOT 4)
 
Authors :  S. Ahmad, S. Muthukumar, A. S. K. Yerabham, V. Kamarthapu, R. Sankarana
Date :  06 Nov 14  (Deposition) - 15 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dtd-Like Fold, Proofreading, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ahmad, S. Muthukumar, S. K. Kuncha, S. B. Routh, A. S. Yerabham, T. Hussain, V. Kamarthapu, S. P. Kruparani, R. Sankaranarayanan
Specificity And Catalysis Hardwired At The Rna-Protein Interface In A Translational Proofreading Enzyme.
Nat Commun V. 6 7552 2015
PubMed-ID: 26113036  |  Reference-DOI: 10.1038/NCOMMS8552

(-) Compounds

Molecule 1 - PROBABLE THREONINE--TRNA LIGASE 2
    Chains: A
    EC Number: 6.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-136
    Gene: THRS2, APE_0117.1
    Organism Scientific: AEROPYRUM PERNIX K1
    Organism Taxid: 272557
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
    Synonym: THREONYL-TRNA SYNTHETASE 2, THRRS 2

 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, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1A3T1Ligand/Ion3'-DEOXY-3'-(L-THREONYLAMINO)ADENOSINE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1A3T2Ligand/Ion3'-DEOXY-3'-(L-THREONYLAMINO)ADENOSINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:40 , VAL A:42 , PRO A:74 , TYR A:75 , ALA A:76 , LEU A:82 , ALA A:83 , ALA A:88 , PHE A:112 , GLY A:113 , TRP A:114 , TYR A:115 , LYS A:116 , GLU A:129 , HOH A:611 , HOH A:643 , HOH A:692 , HOH A:728BINDING SITE FOR RESIDUE A3T A 501
2AC2SOFTWAREHOH A:621 , HOH A:630 , HOH A:631 , HOH A:649 , HOH A:684 , HOH A:722BINDING SITE FOR RESIDUE MG A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RRD)

(-) 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:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh....eeee....eeeeeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrd A   1 MRLLYLHADRFEYKTVKPALKNPPDPPGEASFGEALVVFTTVEDGDGPQTVMYAASDIASHSSRLKVTTVILYPYAHLSSRLAKPMAAHKRLIELEGALRTKFPGHVHRAPFGWYKSFSIACKGHPLAELSRSFTE 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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 4RRD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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
    A3T  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rrd)
 
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
  4rrd
    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
  SYT2_AERPE | Q9YFY3
    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
  SYT2_AERPE | Q9YFY3
    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
        SYT2_AERPE | Q9YFY3: 4rr6 4rr7 4rr8 4rr9 4rra 4rrb 4rrc 4rrh 4rri 4rrj 4rrk 4rrl 4rrm

(-) Related Entries Specified in the PDB File

4rr6 4rr7 4rr8 4rr9 4rra 4rrb 4rrc 4rrf 4rrg 4rrh 4rri 4rrj 4rrk 4rrl 4rrm 4rrq 4rrr