PDB entry 5n5v

View 5n5v on RCSB PDB site
Description: Structure of p-boronophenylalanyl tRNA synthetase - apo form
Class: ligase
Keywords: aminoacylation, ligase, non-natural amino acid, synthetic biology
Deposited on 2017-02-14, released 2018-02-14
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-02-14, with a file datestamp of 2018-02-09.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: N/A
AEROSPACI score: 0.25 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Tyrosine--tRNA ligase
    Species: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) [TaxId:243232]
    Gene: tyrS, MJ0389
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q57834 (0-305)
      • engineered mutation (5)
      • engineered mutation (31)
      • engineered mutation (64)
      • engineered mutation (69)
      • engineered mutation (157)
      • engineered mutation (161)
      • engineered mutation (285)
      • expression tag (306-308)
    Domains in SCOPe 2.07: d5n5va1, d5n5va2
  • Chain 'B':
    Compound: Tyrosine--tRNA ligase
    Species: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) [TaxId:243232]
    Gene: tyrS, MJ0389
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q57834 (0-305)
      • engineered mutation (5)
      • engineered mutation (31)
      • engineered mutation (64)
      • engineered mutation (69)
      • engineered mutation (157)
      • engineered mutation (161)
      • engineered mutation (285)
      • expression tag (306)
    Domains in SCOPe 2.07: d5n5vb1, d5n5vb2
  • Chain 'C':
    Compound: Tyrosine--tRNA ligase
    Species: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) [TaxId:243232]
    Gene: tyrS, MJ0389
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q57834 (0-305)
      • engineered mutation (5)
      • engineered mutation (31)
      • engineered mutation (64)
      • engineered mutation (69)
      • engineered mutation (157)
      • engineered mutation (161)
      • engineered mutation (285)
    Domains in SCOPe 2.07: d5n5vc_
  • Chain 'D':
    Compound: Tyrosine--tRNA ligase
    Species: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) [TaxId:243232]
    Gene: tyrS, MJ0389
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q57834 (0-305)
      • engineered mutation (5)
      • engineered mutation (31)
      • engineered mutation (64)
      • engineered mutation (69)
      • engineered mutation (157)
      • engineered mutation (161)
      • engineered mutation (285)
      • expression tag (306-308)
    Domains in SCOPe 2.07: d5n5vd1, d5n5vd2
  • Chain 'E':
    Compound: Tyrosine--tRNA ligase
    Species: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) [TaxId:243232]
    Gene: tyrS, MJ0389
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q57834 (0-305)
      • engineered mutation (5)
      • engineered mutation (31)
      • engineered mutation (64)
      • engineered mutation (69)
      • engineered mutation (157)
      • engineered mutation (161)
      • engineered mutation (285)
      • expression tag (306-308)
    Domains in SCOPe 2.07: d5n5ve1, d5n5ve2
  • Chain 'F':
    Compound: Tyrosine--tRNA ligase
    Species: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) [TaxId:243232]
    Gene: tyrS, MJ0389
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q57834 (0-305)
      • engineered mutation (5)
      • engineered mutation (31)
      • engineered mutation (64)
      • engineered mutation (69)
      • engineered mutation (157)
      • engineered mutation (161)
      • engineered mutation (285)
      • expression tag (306-308)
    Domains in SCOPe 2.07: d5n5vf1, d5n5vf2
  • Chain 'G':
    Compound: Tyrosine--tRNA ligase
    Species: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) [TaxId:243232]
    Gene: tyrS, MJ0389
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q57834 (0-305)
      • engineered mutation (5)
      • engineered mutation (31)
      • engineered mutation (64)
      • engineered mutation (69)
      • engineered mutation (157)
      • engineered mutation (161)
      • engineered mutation (285)
      • expression tag (306-308)
    Domains in SCOPe 2.07: d5n5vg1, d5n5vg2
  • Chain 'H':
    Compound: Tyrosine--tRNA ligase
    Species: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) [TaxId:243232]
    Gene: tyrS, MJ0389
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q57834 (0-305)
      • engineered mutation (5)
      • engineered mutation (31)
      • engineered mutation (64)
      • engineered mutation (69)
      • engineered mutation (157)
      • engineered mutation (161)
      • engineered mutation (285)
      • expression tag (306)
    Domains in SCOPe 2.07: d5n5vh1, d5n5vh2
  • Heterogens: CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5n5vA (A:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5n5vA (A:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsah
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5n5vB (B:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5n5vB (B:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrls
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5n5vC (C:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5n5vC (C:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5n5vD (D:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5n5vD (D:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsah
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5n5vE (E:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5n5vE (E:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsah
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5n5vF (F:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5n5vF (F:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsah
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5n5vG (G:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5n5vG (G:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsah
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >5n5vH (H:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrlsahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >5n5vH (H:)
    mdefelikrntseiiseeelrevlkkdeksasigfepsgkihlghylqikkmidlqnagf
    diiialadlmaylnqkgeldeirkigdynkkvfeamglkakyvygsefqldkdytlnvyr
    lalkttlkrarrsmeliaredenpkvaeviypimqvnsihyegvdvavggmeqrkihmla
    rellpkkvvcihnpvltgldgegkmssskgnfiavddspeeirakikkaycpagvvegnp
    imeiakyfleypltikrpekfggdltvnsyeeleslfknkelhpmrlknavaeelikile
    pirkrls