PDB entry 6u1j

View 6u1j on RCSB PDB site
Description: Thermus thermophilus D-alanine-D-alanine ligase in complex with ADP, phosphate, D-ala-D-ala, Mg2+ and K+
Class: ligase
Keywords: ATP-grasp domain, ATP binding, metal binding, LIGASE
Deposited on 2019-08-15, released 2020-05-06
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-06-17, with a file datestamp of 2020-06-12.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: N/A
AEROSPACI score: 0.26 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [TaxId:300852]
    Gene: ddl, TTHA1587
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5SHZ3 (2-320)
      • expression tag (321-325)
    Domains in SCOPe 2.08: d6u1ja1, d6u1ja2, d6u1ja3
  • Chain 'B':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [TaxId:300852]
    Gene: ddl, TTHA1587
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5SHZ3 (2-320)
      • expression tag (321-323)
    Domains in SCOPe 2.08: d6u1jb1, d6u1jb2, d6u1jb3
  • Chain 'C':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [TaxId:300852]
    Gene: ddl, TTHA1587
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5SHZ3 (2-320)
      • expression tag (321-325)
    Domains in SCOPe 2.08: d6u1jc1, d6u1jc2, d6u1jc3
  • Chain 'D':
    Compound: d-alanine--d-alanine ligase
    Species: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [TaxId:300852]
    Gene: ddl, TTHA1587
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5SHZ3 (Start-320)
      • expression tag (321-324)
    Domains in SCOPe 2.08: d6u1jd1, d6u1jd2, d6u1jd3
  • Heterogens: DAL, MG, PO4, K, ADP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6u1jA (A:)
memrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaa
pegehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdl
skrvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalal
afrydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraelli
papldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprl
feaggvaypellrrlvelalthhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6u1jA (A:)
mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
rydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraellipa
pldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfe
aggvaypellrrlvelalthhhhh

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6u1jB (B:)
memrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaa
pegehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdl
skrvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalal
afrydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraelli
papldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprl
feaggvaypellrrlvelalthhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6u1jB (B:)
mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgvgisrverfqdleaalalafry
dekavvekalspvrelevgvlgnvfgeaspvgevraellipapldpgtqetvqelalkay
kvlgvrgmarvdfflaegelylnelntipgftptsmyprlfeaggvaypellrrlvelal
thhh

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6u1jC (C:)
memrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaa
pegehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdl
skrvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalal
afrydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraelli
papldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprl
feaggvaypellrrlvelalthhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6u1jC (C:)
mrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaape
gehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlsk
rvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalaf
rydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraellipa
pldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprlfe
aggvaypellrrlvelalthhhhh

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6u1jD (D:)
memrvlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaa
pegehpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdl
skrvlaqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalal
afrydekavvekalspvrelevgvlgnvfgeaspvgevryeapfydyetkytpgraelli
papldpgtqetvqelalkaykvlgvrgmarvdfflaegelylnelntipgftptsmyprl
feaggvaypellrrlvelalthhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6u1jD (D:)
vlliaggvspehevsllsaegvlrhipfptdlaviaqdgrwllgekaltaleakaapege
hpfppplswerydvvfpllhgrfgedgtvqgflellgkpyvgagvaasalcmdkdlskrv
laqagvpvvpwvavrkgeppvvpfdppffvkpantgssvgisrverfqdleaalalafry
dekavvekalspvrelevgvlgnvfgeaspvgevaellipapldpgtqetvqelalkayk
vlgvrgmarvdfflaegelylnelntipgftptsmyprlfeaggvaypellrrlvelalt
hhhh