PDB entry 4kgn

View 4kgn on RCSB PDB site
Description: Crystal structure of a tRNA (cytidine(34)-2'-O)-methyltransferase bound to S-adenosyl homocysteine
Class: transferase
Keywords: Structural Genomics, NIAID, Seattle Structural Genomics Center for Infectious Disease, SSGCID, National Institute for Allergy and Infectious Disease, tRNA methyltransferase, trefoil protein knot, 3(1) protein knot, S-adenosyl-methionine-dependent, SAM, S-adenosylhomocysteine, SAH, half-site occupancy, transferase
Deposited on 2013-04-29, released 2013-05-08
The last revision prior to the SCOPe 2.05 freeze date was dated 2013-05-08, with a file datestamp of 2013-05-03.
Experiment type: XRAY
Resolution: 2.15 Å
R-factor: 0.17
AEROSPACI score: 0.44 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: tRNA (cytidine(34)-2'-O)-methyltransferase
    Species: Burkholderia pseudomallei [TaxId:320372]
    Gene: BURPS1710b_0668, trmL
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4kgna_
  • Chain 'B':
    Compound: tRNA (cytidine(34)-2'-O)-methyltransferase
    Species: Burkholderia pseudomallei [TaxId:320372]
    Gene: BURPS1710b_0668, trmL
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4kgnb_
  • Chain 'C':
    Compound: tRNA (cytidine(34)-2'-O)-methyltransferase
    Species: Burkholderia pseudomallei [TaxId:320372]
    Gene: BURPS1710b_0668, trmL
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q3JWH1 (4-159)
      • expression tag (3)
    Domains in SCOPe 2.05: d4kgnc_
  • Chain 'D':
    Compound: tRNA (cytidine(34)-2'-O)-methyltransferase
    Species: Burkholderia pseudomallei [TaxId:320372]
    Gene: BURPS1710b_0668, trmL
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q3JWH1 (4-159)
      • expression tag (2-3)
    Domains in SCOPe 2.05: d4kgnd_
  • Chain 'E':
    Compound: tRNA (cytidine(34)-2'-O)-methyltransferase
    Species: Burkholderia pseudomallei [TaxId:320372]
    Gene: BURPS1710b_0668, trmL
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4kgne_
  • Chain 'F':
    Compound: tRNA (cytidine(34)-2'-O)-methyltransferase
    Species: Burkholderia pseudomallei [TaxId:320372]
    Gene: BURPS1710b_0668, trmL
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q3JWH1 (4-159)
      • expression tag (2-3)
    Domains in SCOPe 2.05: d4kgnf_
  • Chain 'G':
    Compound: tRNA (cytidine(34)-2'-O)-methyltransferase
    Species: Burkholderia pseudomallei [TaxId:320372]
    Gene: BURPS1710b_0668, trmL
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4kgng_
  • Chain 'H':
    Compound: tRNA (cytidine(34)-2'-O)-methyltransferase
    Species: Burkholderia pseudomallei [TaxId:320372]
    Gene: BURPS1710b_0668, trmL
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4kgnh_
  • Heterogens: SAH, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4kgnA (A:)
gpgsmfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaq
mrvhrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrf
apeqrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

    Sequence, based on observed residues (ATOM records): (download) 
    >4kgnA (A:)
mfnvvlvepeippntgnvirlcantgarlhlieplgfpqmrvhrdwdafvaaeapdparm
fafttrgsgrfhdrafepgdwfvfgaetrglapalvdrfapeqrvrlpmrpgnrslnlsn
tvavvvfeawrqagfegga

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4kgnB (B:)
gpgsmfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaq
mrvhrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrf
apeqrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

    Sequence, based on observed residues (ATOM records): (download) 
    >4kgnB (B:)
mfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaqmrvh
rdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrfapeq
rvrlpmrpgnrslnlsntvavvvfeawrqagfegga

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4kgnC (C:)
gpgsmfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaq
mrvhrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrf
apeqrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

    Sequence, based on observed residues (ATOM records): (download) 
    >4kgnC (C:)
smfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaqmrv
hrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrfape
qrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4kgnD (D:)
gpgsmfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaq
mrvhrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrf
apeqrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

    Sequence, based on observed residues (ATOM records): (download) 
    >4kgnD (D:)
gsmfnvvlvepeippntgnvirlcantgarlhlieplgfplgldyheyaqmrvhrdwdaf
vaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrfapeqrvrlpm
rpgnrslnlsntvavvvfeawrqagfegga

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4kgnE (E:)
gpgsmfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaq
mrvhrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrf
apeqrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

    Sequence, based on observed residues (ATOM records): (download) 
    >4kgnE (E:)
mfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaqmrvh
rdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrfapeq
rvrlpmrpgnrslnlsntvavvvfeawrqagfegga

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >4kgnF (F:)
gpgsmfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaq
mrvhrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrf
apeqrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

    Sequence, based on observed residues (ATOM records): (download) 
    >4kgnF (F:)
gsmfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaqmr
vhrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrfap
eqrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >4kgnG (G:)
gpgsmfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaq
mrvhrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrf
apeqrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

    Sequence, based on observed residues (ATOM records): (download) 
    >4kgnG (G:)
mfnvvlvepeippntgnvirlcantgarlhlieplgfplgldyheyaqmrvhrdwdafva
aeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrfapeqrvrlpmrp
gnrslnlsntvavvvfeawrqagfegga

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >4kgnH (H:)
gpgsmfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaq
mrvhrdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrf
apeqrvrlpmrpgnrslnlsntvavvvfeawrqagfegga

    Sequence, based on observed residues (ATOM records): (download) 
    >4kgnH (H:)
mfnvvlvepeippntgnvirlcantgarlhlieplgfplddakmrragldyheyaqmrvh
rdwdafvaaeapdparmfafttrgsgrfhdrafepgdwfvfgaetrglapalvdrfapeq
rvrlpmrpgnrslnlsntvavvvfeawrqagfegga