PDB entry 5jvl

View 5jvl on RCSB PDB site
Description: C4-type pyruvate phospate dikinase: nucleotide binding domain with bound ATP analogue
Class: transferase
Keywords: phosphotransferase, nucleotide binding, conformational transition, swiveling mechanism, transferase
Deposited on 2016-05-11, released 2017-04-05
The last revision prior to the SCOPe 2.06 freeze date was dated 2017-04-05, with a file datestamp of 2017-03-31.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: N/A
AEROSPACI score: 0.16 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Pyruvate, phosphate dikinase, chloroplastic
    Species: Flaveria trinervia [TaxId:4227]
    Gene: PPDK, PDK
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5jvla1, d5jvla2, d5jvla3
  • Chain 'B':
    Compound: Pyruvate, phosphate dikinase, chloroplastic
    Species: Flaveria trinervia [TaxId:4227]
    Gene: PPDK, PDK
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5jvlb1
  • Chain 'C':
    Compound: Pyruvate, phosphate dikinase, chloroplastic
    Species: Flaveria trinervia [TaxId:4227]
    Gene: PPDK, PDK
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5jvlc1, d5jvlc2, d5jvlc3
  • Chain 'D':
    Compound: Pyruvate, phosphate dikinase, chloroplastic
    Species: Flaveria trinervia [TaxId:4227]
    Gene: PPDK, PDK
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5jvld1, d5jvld2, d5jvld3
  • Heterogens: 6NQ, MG, PEP

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5jvlA (A:)
kkrvftfgkgrsegnrdmksllggkganlaemssiglsvppgltisteaceeyqqngksl
ppglwdeisegldyvqkemsaslgdpskplllsvrsgaaismpgmmdtvlnlglndevva
glagksgarfaydsyrrfldmfgnvvmgiphslfdekleqmkaekgihldtdltaadlkd
lvekyknvyveakgekfptdpkkqlelavnavfdswdsprankyrsinqitglkgtavni
qsmvfgnmgntsgtgvlftrnpstgekklygeflinaqgedvvagirtpedlgtmetcmp
eaykelvenceilerhykdmmdieftvqenrlwmlqcrtgkrtgkgavriavdmvnegli
dtrtaikrvetqhldqllhpqfedpsaykshvvatglpaspgaavgqvcfsaedaetwha
qgksailvrtetspedvggmhaaagiltarggmtshaavvargwgkccvsgcadirvndd
mkiftigdrvikegdwlslngttgevilgkqllappamsndleifmswadqarrlkvman
adtpndaltarnngaqgiglcrtehmffasderikavrkmimavtpeqrkvaldlllpyq
rsdfegiframdglpvtirlldpplheflpegdlehivnelavdtgmsadeiyskienls
evnpmlgfrgcrlgisypeltemqvraifqaavsmtnqgvtvipeimvplvgtpqelrhq
isvirgvaanvfaemgvtleykvgtmieipraaliaeeigkeadffsfgtndltqmtfgy
srddvgkflqiylaqgilqhdpfevidqkgvgqlikmatekgraanpslkvgicgehgge
pssvaffdgvgldyvscspfrvpiarlaaaqviv

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5jvlB (B:)
kkrvftfgkgrsegnrdmksllggkganlaemssiglsvppgltisteaceeyqqngksl
ppglwdeisegldyvqkemsaslgdpskplllsvrsgaaismpgmmdtvlnlglndevva
glagksgarfaydsyrrfldmfgnvvmgiphslfdekleqmkaekgihldtdltaadlkd
lvekyknvyveakgekfptdpkkqlelavnavfdswdsprankyrsinqitglkgtavni
qsmvfgnmgntsgtgvlftrnpstgekklygeflinaqgedvvagirtpedlgtmetcmp
eaykelvenceilerhykdmmdieftvqenrlwmlqcrtgkrtgkgavriavdmvnegli
dtrtaikrvetqhldqllhpqfedpsaykshvvatglpaspgaavgqvcfsaedaetwha
qgksailvrtetspedvggmhaaagiltarggmtshaavvargwgkccvsgcadirvndd
mkiftigdrvikegdwlslngttgevilgkqllappamsndleifmswadqarrlkvman
adtpndaltarnngaqgiglcrtehmffasderikavrkmimavtpeqrkvaldlllpyq
rsdfegiframdglpvtirlldpplheflpegdlehivnelavdtgmsadeiyskienls
evnpmlgfrgcrlgisypeltemqvraifqaavsmtnqgvtvipeimvplvgtpqelrhq
isvirgvaanvfaemgvtleykvgtmieipraaliaeeigkeadffsfgtndltqmtfgy
srddvgkflqiylaqgilqhdpfevidqkgvgqlikmatekgraanpslkvgicgehgge
pssvaffdgvgldyvscspfrvpiarlaaaqviv

    Sequence, based on observed residues (ATOM records): (download) 
    >5jvlB (B:)
ftrnpstgekklylvenceilerhykdmmdirtgkrtgkgavriavdmvneglidtrtai
krvetqhldqllhpqfedpsaykshvvatglpaspgaavgqvcfsaedaetwhaqgksai
lmtshaavvargwgkccvegdwlslngttgevilgkqllappamsndleifmswadqarr
lkvmanadtpndaltarnngaqgiglcrtehmffasderikavrkmimavtpeqrkvald
lllpyqrsdfegiframdglpvtirlldpplheflpegdlehivnelavdtgmsadeiys
kienlsevnpmlgfrgcrlgisypeltemqvraifqaavsmtnqgvtvipeimvplvgtp
qelrhqisvirgvaanvfaemgvtleykvgtmieipraaliaeeigkeadffsfgtndlt
qmtfgysrddvgkflqiylaqgilqhdpfevidqkgvgqlikmatekgraanpslkvgic
gehggepssvaffdgvgldyvscspfrvpiarlaaaqviv

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5jvlC (C:)
kkrvftfgkgrsegnrdmksllggkganlaemssiglsvppgltisteaceeyqqngksl
ppglwdeisegldyvqkemsaslgdpskplllsvrsgaaismpgmmdtvlnlglndevva
glagksgarfaydsyrrfldmfgnvvmgiphslfdekleqmkaekgihldtdltaadlkd
lvekyknvyveakgekfptdpkkqlelavnavfdswdsprankyrsinqitglkgtavni
qsmvfgnmgntsgtgvlftrnpstgekklygeflinaqgedvvagirtpedlgtmetcmp
eaykelvenceilerhykdmmdieftvqenrlwmlqcrtgkrtgkgavriavdmvnegli
dtrtaikrvetqhldqllhpqfedpsaykshvvatglpaspgaavgqvcfsaedaetwha
qgksailvrtetspedvggmhaaagiltarggmtshaavvargwgkccvsgcadirvndd
mkiftigdrvikegdwlslngttgevilgkqllappamsndleifmswadqarrlkvman
adtpndaltarnngaqgiglcrtehmffasderikavrkmimavtpeqrkvaldlllpyq
rsdfegiframdglpvtirlldpplheflpegdlehivnelavdtgmsadeiyskienls
evnpmlgfrgcrlgisypeltemqvraifqaavsmtnqgvtvipeimvplvgtpqelrhq
isvirgvaanvfaemgvtleykvgtmieipraaliaeeigkeadffsfgtndltqmtfgy
srddvgkflqiylaqgilqhdpfevidqkgvgqlikmatekgraanpslkvgicgehgge
pssvaffdgvgldyvscspfrvpiarlaaaqviv

    Sequence, based on observed residues (ATOM records): (download) 
    >5jvlC (C:)
kkrvftfgkgrsegnrdmksllggkganlaemssiglsvppgltisteaceeyqqngksl
ppglwdeisegldyvqkemsaslgdpskplllsvrsgaaismpgmmdtvlnlglndevva
glagksgarfaydsyrrfldmfgnvvmgiphslfdekleqmkaekgihldtdltaadlkd
lvekyknvyveakgekfptdpkkqlelavnavfdswdlkgtavniqsmvfgnmgntsgtg
vlftrnpstgekklygeflinaqgedvvagirtpedlgtmetcmpeaykelvenceiler
hykdmmdieftvqenrlwmlqcrtgkrtgkgavriavdmvneglidtrtaikrvetqhld
qllhpqfedpsaykshvvatglpaspgaavgqvcfsaedaetwhaqgksailvrtetspe
dvggmhaaagiltarggmtshaavvargwgkccvsgcadirvnddmkiftigdrvikegd
wlslngttgevilgkqllappamsndleifmswadqarrlkvmanadtpndaltarnnga
qgiglcrtehmffasderikavrkmimavtpeqrkvaldlllpyqrsdfegiframdglp
vtirlldpplheflpegdlehivnelavdtgmsadeiyskienlsevnpmlgfrgcrlgi
sypeltemqvraifqaavsmtnqgvtvipeimvplvgtpqelrhqisvirgvaanvfaem
gvtleykvgtmieipraaliaeeigkeadffsfgtndltqmtfgysrddvgkflqiylaq
gilqhdpfevidqkgvgqlikmatekgraanpslkvgicgehggepssvaffdgvgldyv
scspfrvpiarlaaaqviv

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5jvlD (D:)
kkrvftfgkgrsegnrdmksllggkganlaemssiglsvppgltisteaceeyqqngksl
ppglwdeisegldyvqkemsaslgdpskplllsvrsgaaismpgmmdtvlnlglndevva
glagksgarfaydsyrrfldmfgnvvmgiphslfdekleqmkaekgihldtdltaadlkd
lvekyknvyveakgekfptdpkkqlelavnavfdswdsprankyrsinqitglkgtavni
qsmvfgnmgntsgtgvlftrnpstgekklygeflinaqgedvvagirtpedlgtmetcmp
eaykelvenceilerhykdmmdieftvqenrlwmlqcrtgkrtgkgavriavdmvnegli
dtrtaikrvetqhldqllhpqfedpsaykshvvatglpaspgaavgqvcfsaedaetwha
qgksailvrtetspedvggmhaaagiltarggmtshaavvargwgkccvsgcadirvndd
mkiftigdrvikegdwlslngttgevilgkqllappamsndleifmswadqarrlkvman
adtpndaltarnngaqgiglcrtehmffasderikavrkmimavtpeqrkvaldlllpyq
rsdfegiframdglpvtirlldpplheflpegdlehivnelavdtgmsadeiyskienls
evnpmlgfrgcrlgisypeltemqvraifqaavsmtnqgvtvipeimvplvgtpqelrhq
isvirgvaanvfaemgvtleykvgtmieipraaliaeeigkeadffsfgtndltqmtfgy
srddvgkflqiylaqgilqhdpfevidqkgvgqlikmatekgraanpslkvgicgehgge
pssvaffdgvgldyvscspfrvpiarlaaaqviv