PDB entry 5vl1

View 5vl1 on RCSB PDB site
Description: Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine
Class: ligase
Keywords: SSGCID, synthetase, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, LIGASE
Deposited on 2017-04-24, released 2017-05-10
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-05-10, with a file datestamp of 2017-05-05.
Experiment type: XRAY
Resolution: 2.7 Å
R-factor: N/A
AEROSPACI score: 0.18 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Lysine--tRNA ligase
    Species: Mycobacterium ulcerans (strain Agy99) [TaxId:362242]
    Gene: lysS, MUL_4181
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5vl1a1, d5vl1a2
  • Chain 'B':
    Compound: Lysine--tRNA ligase
    Species: Mycobacterium ulcerans (strain Agy99) [TaxId:362242]
    Gene: lysS, MUL_4181
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5vl1b1, d5vl1b2
  • Chain 'C':
    Compound: Lysine--tRNA ligase
    Species: Mycobacterium ulcerans (strain Agy99) [TaxId:362242]
    Gene: lysS, MUL_4181
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5vl1c1, d5vl1c2
  • Chain 'D':
    Compound: Lysine--tRNA ligase
    Species: Mycobacterium ulcerans (strain Agy99) [TaxId:362242]
    Gene: lysS, MUL_4181
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5vl1d1, d5vl1d2
  • Heterogens: PGE, LYS, PEG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5vl1A (A:)
mahhhhhhmssaesnipeqfrirrdkrarllaegydpypvaierthtlaeiratyadlpt
dsatedivgvagrvvfarntgklcfatlqdgdgtqlqamisldevgresldrwkadvdig
dvvyvhgtvissrrgelsvladswrmaakalrplpvahkemseesrvrqryvdlivrpqa
revarqriaviravrnalerrgflevetpmlqtlaggaaarpfvthsnaldidlylriap
elflkrcivggfdrvfelnrvfrnegsdsthspefsmletyqtygtyddsalitreliqe
vadeaigtrqlsmpdgsvydidgewatmemysslsealgeqitpettvarlrdiasgldv
eidnsvfghgklveelwehavgnkltaptfvkdfpvettpltrqhrsipgvtekwdlyvr
gvelatgyselndpvvqrdrfadqaraaaagddeamqldedfltaleygmppctgtgmgi
drllmcltglsiretvlfpivrphsn

    Sequence, based on observed residues (ATOM records): (download) 
    >5vl1A (A:)
peqfrirrdkrarllaegydpypvaierthtlaeiratyadlptdsatedivgvagrvvf
arntgklcfatlqdgdgtqlqamisldevgresldrwkadvdigdvvyvhgtvissrrge
lsvladswrmaakalrplpvahkemseesrvrqryvdlivrpqarevarqriaviravrn
alerrgflevetpmlqtlaggaaarpfvthsnaldidlylriapelflkrcivggfdrvf
elnrvfrnegsdsthspefsmletyqtygtyddsalitreliqevadeaigtrqlsmpdg
svydidgewatmemysslsealgeqitpettvarlrdiasgldveidnsvfghgklveel
wehavgnkltaptfvkdfpvettpltrqhrsipgvtekwdlyvrgvelatgyselndpvv
qrdrfadqaraaaagddeamqldedfltaleygmppctgtgmgidrllmcltglsiretv
lfpivr

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5vl1B (B:)
mahhhhhhmssaesnipeqfrirrdkrarllaegydpypvaierthtlaeiratyadlpt
dsatedivgvagrvvfarntgklcfatlqdgdgtqlqamisldevgresldrwkadvdig
dvvyvhgtvissrrgelsvladswrmaakalrplpvahkemseesrvrqryvdlivrpqa
revarqriaviravrnalerrgflevetpmlqtlaggaaarpfvthsnaldidlylriap
elflkrcivggfdrvfelnrvfrnegsdsthspefsmletyqtygtyddsalitreliqe
vadeaigtrqlsmpdgsvydidgewatmemysslsealgeqitpettvarlrdiasgldv
eidnsvfghgklveelwehavgnkltaptfvkdfpvettpltrqhrsipgvtekwdlyvr
gvelatgyselndpvvqrdrfadqaraaaagddeamqldedfltaleygmppctgtgmgi
drllmcltglsiretvlfpivrphsn

    Sequence, based on observed residues (ATOM records): (download) 
    >5vl1B (B:)
ipeqfrirrdkrarllaegydpypvaierthtlaeiratyadlptdsatedivgvagrvv
farntgklcfatlqdgdgtqlqamisldevgresldrwkadvdigdvvyvhgtvissrrg
elsvladswrmaakalrplpvkemseesrvrqryvdlivrpqarevarqriaviravrna
lerrgflevetpmlqtlaggaaarpfvthsnaldidlylriapelflkrcivggfdrvfe
lnrvfrnegsdsthspefsmletyqtygtyddsalitreliqevadeaigtrqlsmpdgs
vydidgewatmemysslsealgeqitpettvarlrdiasgldveidnsvfghgklveelw
ehavgnkltaptfvkdfpvettpltrqhrsipgvtekwdlyvrgvelatgyselndpvvq
rdrfadqaraaaagddeamqldedfltaleygmppctgtgmgidrllmcltglsiretvl
fpivr

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5vl1C (C:)
mahhhhhhmssaesnipeqfrirrdkrarllaegydpypvaierthtlaeiratyadlpt
dsatedivgvagrvvfarntgklcfatlqdgdgtqlqamisldevgresldrwkadvdig
dvvyvhgtvissrrgelsvladswrmaakalrplpvahkemseesrvrqryvdlivrpqa
revarqriaviravrnalerrgflevetpmlqtlaggaaarpfvthsnaldidlylriap
elflkrcivggfdrvfelnrvfrnegsdsthspefsmletyqtygtyddsalitreliqe
vadeaigtrqlsmpdgsvydidgewatmemysslsealgeqitpettvarlrdiasgldv
eidnsvfghgklveelwehavgnkltaptfvkdfpvettpltrqhrsipgvtekwdlyvr
gvelatgyselndpvvqrdrfadqaraaaagddeamqldedfltaleygmppctgtgmgi
drllmcltglsiretvlfpivrphsn

    Sequence, based on observed residues (ATOM records): (download) 
    >5vl1C (C:)
ipeqfrirrdkrarllaegydpypvaierthtlaeiratyadlptdsatedivgvagrvv
farntgklcfatlqdgdgtqlqamisldevgresldrwkadvdigdvvyvhgtvissrrg
elsvladswrmaakalrplpvahkemseesrvrqryvdlivrpqarevarqriaviravr
nalerrgflevetpmlqtlaggaaarpfvthsnaldidlylriapelflkrcivggfdrv
felnrvfrnegsdsthspefsmletyqtygtyddsalitreliqevadeaigtrqlsmpd
gsvydidgewatmemysslsealgeqitpettvarlrdiasgldveidnsvfghgklvee
lwehavgnkltaptfvkdfpvettpltrqhrsipgvtekwdlyvrgvelatgyselndpv
vqrdrfadqaraaaagddeamqldedfltaleygmppctgtgmgidrllmcltglsiret
vlfpivr

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5vl1D (D:)
mahhhhhhmssaesnipeqfrirrdkrarllaegydpypvaierthtlaeiratyadlpt
dsatedivgvagrvvfarntgklcfatlqdgdgtqlqamisldevgresldrwkadvdig
dvvyvhgtvissrrgelsvladswrmaakalrplpvahkemseesrvrqryvdlivrpqa
revarqriaviravrnalerrgflevetpmlqtlaggaaarpfvthsnaldidlylriap
elflkrcivggfdrvfelnrvfrnegsdsthspefsmletyqtygtyddsalitreliqe
vadeaigtrqlsmpdgsvydidgewatmemysslsealgeqitpettvarlrdiasgldv
eidnsvfghgklveelwehavgnkltaptfvkdfpvettpltrqhrsipgvtekwdlyvr
gvelatgyselndpvvqrdrfadqaraaaagddeamqldedfltaleygmppctgtgmgi
drllmcltglsiretvlfpivrphsn

    Sequence, based on observed residues (ATOM records): (download) 
    >5vl1D (D:)
nipeqfrirrdkrarllaegydpypvaierthtlaeiratyadlptdsatedivgvagrv
vfarntgklcfatlqdgdgtqlqamisldevgresldrwkadvdigdvvyvhgtvissrr
gelsvladswrmaakalrplpvkemseesrvrqryvdlivrpqarevarqriaviravrn
alerrgflevetpmlqtlaggaaarpfvthsnaldidlylriapelflkrcivggfdrvf
elnrvfrnegsdsthspefsmletyqtygtyddsalitreliqevadeaigtrqlsmpdg
svydidgewatmemysslsealgeqitpettvarlrdiasgldvesvfghgklveelweh
avgnkltaptfvkdfpvettpltrqhrsipgvtekwdlyvrgvelatgyselndpvvqrd
rfadqaraaaagddeamqldedfltaleygmppctgtgmgidrllmcltglsiretvlfp
ivr