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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM METHANOCOCCUS JANNASCHII WITH L-SER3AA
 
Authors :  S. Ahmad, A. S. K. Yerabham, V. Kamarthapu, R. Sankaranarayanan
Date :  06 Nov 14  (Deposition) - 15 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  E,F  (1x)
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 - THREONINE--TRNA LIGASE
    Chains: A, B, C, D, E, F
    EC Number: 6.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-141
    Gene: THRS, MJ1197
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
    Synonym: THREONYL-TRNA SYNTHETASE, THRRS

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  BC   
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1A3S6Ligand/IonSERINE-3'-AMINOADENOSINE
2CL1Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1A3S2Ligand/IonSERINE-3'-AMINOADENOSINE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1A3S2Ligand/IonSERINE-3'-AMINOADENOSINE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1A3S2Ligand/IonSERINE-3'-AMINOADENOSINE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:25 , ILE A:44 , VAL A:46 , PRO A:81 , TYR A:82 , ALA A:83 , HIS A:84 , LEU A:89 , SER A:90 , ALA A:95 , PHE A:118 , GLY A:119 , TRP A:120 , TYR A:121 , LYS A:122 , HOH A:607 , HOH A:686 , GLU D:135 , HOH D:301BINDING SITE FOR RESIDUE A3S A 501
2AC2SOFTWAREGLU A:27 , THR A:29 , ARG A:115 , PHE A:118BINDING SITE FOR RESIDUE CL A 502
3AC3SOFTWAREILE B:44 , VAL B:46 , PRO B:81 , TYR B:82 , ALA B:83 , LEU B:89 , SER B:90 , ALA B:95 , PHE B:118 , GLY B:119 , TYR B:121 , HOH B:304 , HOH B:321 , HOH B:361 , GLU C:135BINDING SITE FOR RESIDUE A3S B 201
4AC4SOFTWAREGLU B:135 , ILE C:25 , ILE C:44 , VAL C:46 , TYR C:82 , ALA C:83 , LEU C:89 , SER C:90 , ALA C:95 , PHE C:118 , GLY C:119 , HOH C:303 , HOH C:342BINDING SITE FOR RESIDUE A3S C 201
5AC5SOFTWAREHOH B:333 , HOH B:363 , HOH C:322 , HOH C:329 , HOH C:355BINDING SITE FOR RESIDUE MG C 202
6AC6SOFTWAREGLU A:135 , ILE D:25 , ILE D:44 , VAL D:46 , TYR D:82 , ALA D:83 , HIS D:84 , LEU D:89 , SER D:90 , ALA D:95 , PHE D:118 , GLY D:119 , HOH D:302 , HOH D:315 , HOH D:374BINDING SITE FOR RESIDUE A3S D 201
7AC7SOFTWAREHOH A:627 , HOH D:305 , HOH D:316 , HOH D:333 , HOH D:350 , HOH D:366BINDING SITE FOR RESIDUE MG D 202
8AC8SOFTWAREILE E:25 , ILE E:44 , VAL E:46 , PRO E:81 , TYR E:82 , ALA E:83 , HIS E:84 , LEU E:89 , SER E:90 , ALA E:95 , PHE E:118 , GLY E:119 , TYR E:121 , HOH E:309 , HOH E:333 , HOH E:354 , GLU F:135BINDING SITE FOR RESIDUE A3S E 201
9AC9SOFTWAREGLU E:135 , ILE F:25 , ILE F:44 , ALA F:45 , VAL F:46 , TYR F:82 , ALA F:83 , HIS F:84 , SER F:90 , ALA F:95 , PHE F:118 , GLY F:119 , TYR F:121 , LYS F:122 , HOH F:306BINDING SITE FOR RESIDUE A3S F 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RRF)

(-) 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..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rrf A   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIVA 142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134        


Chain B from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrf B   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIV 141
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       


Chain C from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrf C   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIVAK 143
                                    14        24        34        44        54        64        74        84        94       104       114       124       134         


Chain D from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrf D   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIVAK 143
                                    14        24        34        44        54        64        74        84        94       104       114       124       134         


Chain E from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhhh.eeee....eeeeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrf E   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIVAKE 144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144


Chain F from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee..........eeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhh....hhhhhhhhhhhhhhhhhhh..eeee....eeeeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrf F   5 MKMLLIHSDYLEFEAKEKTKIAEETENLKGKLDECLACFIAVEREDENNPEGTAIGAVEEIEKVANQLKVNNIVVYPYAHLSSDLSSPETAVKVLKDIESILKERGYNVLRAPFGWYKAFKISCKGHPLSELSRKIVAKE 144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144
   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 4RRF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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
    A3S  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4rrf)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  4rrf
    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_METJA | Q58597
    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_METJA | Q58597
    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_METJA | Q58597: 4rrg

(-) Related Entries Specified in the PDB File

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