PDB entry 3dxj

View 3dxj on RCSB PDB site
Description: Crystal structure of thermus thermophilus rna polymerase holoenzyme in complex with the antibiotic myxopyronin
Class: transcription,transferase
Keywords: RNA POLYMERASE; RNAP; DRUG COMPLEX; INHIBITOR; corallopyronin; ripostatin; TRANSCRIPTION; HOLOENZYME; CRYSTALLOGRAPHY; TWINNING; HEMIHEDRAL, DNA-directed RNA polymerase, Nucleotidyltransferase, Transcription, Transferase, DNA-binding, Sigma factor, Transcription regulation, TRANSCRIPTION,TRANSFERASE
Deposited on 2008-07-24, released 2008-10-14
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-02-24, with a file datestamp of 2009-02-03.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.235
AEROSPACI score: 0.15 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: bactrial RNA polymerase beta subunit; chain c, m
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dxjc_
  • Chain 'D':
    Compound: bactrial RNA polymerase beta-prime subunit; chain d, n
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dxjd_
  • Chain 'E':
    Compound: bactrial RNA polymerase omega subunit; chain e, o
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8RQE7
      • variant (60)
      • variant (91)
      • variant (94)
    Domains in SCOPe 2.06: d3dxje_
  • Chain 'F':
    Compound: RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dxjf1, d3dxjf2, d3dxjf3
  • Chain 'K':
    Compound: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: DNA-directed RNA polymerase subunit alpha; CHAIN A, B, K, L
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: bactrial RNA polymerase beta subunit; chain c, m
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dxjm_
  • Chain 'N':
    Compound: bactrial RNA polymerase beta-prime subunit; chain d, n
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dxjn_
  • Chain 'O':
    Compound: bactrial RNA polymerase omega subunit; chain e, o
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8RQE7
      • variant (60)
      • variant (91)
      • variant (94)
    Domains in SCOPe 2.06: d3dxjo_
  • Chain 'P':
    Compound: RNA polymerase pricipal sigma factor (RpoD); CHAIN F, P
    Species: Thermus thermophilus HB8 [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dxjp1, d3dxjp2, d3dxjp3
  • Heterogens: PO4, MG, ZN, NE6, MPD, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dxjC (C:)
meikrfgrireviplpplteiqvesyrralqadvppekrenvgiqaafretfpieeedkg
kgglvldfleyrlgeppfpqdecrekdltyqaplyarlqlihkdtglikedevflghipl
mtedgsfiingadrvivsqihrspgvyftpdparpgryiasiiplpkrgpwidlevepng
vvsmkvnkrkfplvlllrvlgydqetlarelgaygelvqglmdesvfamrpeealirlft
llrpgdppkrdkavayvygliadprrydlgeagrykaeeklgirlsgrtlarfedgefkd
evflptlrylfaltagvpghevddidhlgnrrirtvgelmtdqfrvglarlargvrerml
mgsedsltpaklvnsrpleaaireffsrsqlsqfkdetnplsslrhkrrisalgpggltr
eragfdvrdvhrthygricpvetpeganiglitslaayarvdelgfirtpyrrvvggvvt
devvymtateedrytiaqantplegnriaaervvarrkgepvivspeevefmdvspkqvf
svntnlipflehddanralmgsnmqtqavpliraqapvvmtgleervvrdslaalyaeed
gevakvdgnrivvryedgrlveyplrrfyrsnqgtaldqrprvvvgqrvrkgdlladgpa
sengflalgqnvlvaimpfdgynfedaiviseellkrdfytsihieryeieardtklgpe
ritrdiphlseaalrdldeegvvrigaevkpgdilvgrtsfkgeseptpeerllrsifge
kardvkdtslrvppgeggivvrtvrlrrgdpgvelkpgvrevvrvyvaqkrklqvgdkla
nrhgnkgvvakilpvedmphlpdgtpvdvilnplgvpsrmnlgqilethlglagyflgqr
yispifdgakepeikellaqafevyfgkrkgegfgvdkrevevlrraeklglvtpgktpe
eqlkelflqgkvvlydgrtgepiegpivvgqmfimklyhmvedkmharstgpyslitqqp
lggkaqfggqrfgemevwaleaygaahtlqemltlksddiegrnaayeaiikgedvpeps
vpesfrvlvkelqalaldvqtldekdnpvdifeglaskr

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3dxjD (D:)
mkkevrkvrialaspekirswsygevekpetinyrtlkperdglfderifgpikdyecac
gkykrqrfegkvcercgvevtksivrryrmghielatpaahiwfvkdvpskigtlldlsa
teleqvlyfskyivldpkgailngvpvekrqlltdeeyrelrygkqetyplppgvdalvk
dgeevvkgqelapgvvsrldgvalyrfprrvrveyvkkeraglrlplaawvekeaykpge
ilaelpepylfraeeegvvelkeleegaflvlrredepvatyflpvgmtplvvhgeivek
gqplaeakgllrmprqvraaqveaeeegetvyltlflewtepkdyrvqphmnvvvpegar
veagdkivaaidpeeeviaeaegvvhlhepasilvvkarvypfeddvevstgdrvapgdv
ladggkvksdvygrvevdlvrnvvrvvesydidarmgaeaiqqllkeldlealekellee
mkhpsrarrakarkrlevvrafldsgnrpewmileavpvlppdlrpmvqvdggrfatsdl
ndlyrrlinrnnrlkkllaqgapeiiirnekrmlqeavdalldngrrgapvtnpgsdrpl
rsltdilsgkqgrfrqnllgkrvdysgrsvivvgpqlklhqcglpkrmalelfkpfllkk
meekgiapnvkaarrmlerqrdikdevwdaleevihgkvvllnraptlhrlgiqafqpvl
vegqsiqlhplvceafnadfdgdqmavhvplssfaqaeariqmlsahnllspasgeplak
psrdiilglyyitqvrkekkgaglefatpeealaahergevalnapikvagretsvgrlk
yvfanpdeallavahgivdlqdvvtvrymgkrletspgrilfarivaeavedekvaweli
qldvpqeknslkdlvyqaflrlgmektarlldalkyygftfsttsgitigiddavipeek
kqyleeadrkllqieqayemgfltdrerydqilqlwtettekvtqavfknfeenypfnpl
yvmaqsgargnpqqirqlcglrglmqkpsgetfevpvrssfregltvleyfisshgarkg
gadtalrtadsgyltrklvdvtheivvreadcgttnyisvplfqpdevtrslrlrkradi
eaglygrvlarevevlgvrleegrylsmddvhllikaaeageiqevpvrspltcqtrygv
cqkcygydlsmarpvsigeavgivaaqsigepgtqltmrtfhtggvagaaditqglprvi
elfearrpkakaviseidgvvrieeteeklsvfvesegfskeyklpkearllvkdgdyve
agqpltrgaidphqlleakgpeaverylveeiqkvyraqgvklhdkhieivvrqmmkyve
vtdpgdsrllegqvlekwdvealnerliaegktpvawkpllmgvtksalstkswlsaasf
qntthvlteaaiagkkdeliglkenvilgrlipagtgsdfvrftqvvdqktlkaieeark
eaveakerpaarrgvkreqpgkqa

    Sequence, based on observed residues (ATOM records): (download) 
    >3dxjD (D:)
kkevrkvrialaspekirswsygevekpetinyrtlkperdglfderifgpikdyecacg
kykrqrfegkvcercgvevtksivrryrmghielatpaahiwfvkdvpskigtlldlsat
eleqvlyfskyivldpkgailngvpvekrqlltdeeyrelrygkqetyplppgvdalvkd
geevvkgqelapgvvsrldgvalyrfprrvrveyvkkeraglrlplaawvekeaykpgei
laelpepylfraeeegvvelkeleegaflvlrredepvatyflpvgmtplvvhgeivekg
qplaeakgllrmprqvraaqveaeeegetvyltlflewtepkdyrvqphmnvvvpegarv
eagdkivaaidpeeeviaeaegvvhlhepasilvvkarvypfeddvevstgdrvapgdvl
adggkvksdvygrvevdlvrnvvrvvesydidarmgaeaiqqllkeldlealekelleem
khpsrarrakarkrlevvrafldsgnrpewmileavpvlppdlrpmvqvdggrfatsdln
dlyrrlinrnnrlkkllaqgapeiiirnekrmlqeavdalldngrrgapvtnpgsdrplr
sltdilsgkqgrfrqnllgkrvdysgrsvivvgpqlklhqcglpkrmalelfkpfllkkm
eekgiapnvkaarrmlerqrdikdevwdaleevihgkvvllnraptlhrlgiqafqpvlv
egqsiqlhplvceafnadfdgdqmavhvplssfaqaeariqmlsahnllspasgeplakp
srdiilglyyitqvrkekkgaglefatpeealaahergevalnapikvagretsvgrlky
vfanpdeallavahgivdlqdvvtvrymgkrletspgrilfarivaeavedekvaweliq
ldvpqeknslkdlvyqaflrlgmektarlldalkyygftfsttsgitigiddavipeekk
qyleeadrkllqieqayemgfltdrerydqilqlwtettekvtqavfknfeenypfnply
vmaqsgargnpqqirqlcglrglmqkpsgetfevpvrssfregltvleyfisshgarkgg
adtalrtadsgyltrklvdvtheivvreadcgttnyisvplfqpdevtrslrlrkradie
aglygrvlarevevlgvrleegrylsmddvhllikaaeageiqevpvrspltcqtrygvc
qkcygydlsmarpvsigeavgivaaqsigepgtqltmrtfhtggvagaaditqglprvie
lfearrpkakaviseidgvvrieeteeklsvfvesegfskeyklpkearllvkdgdyvea
gqpltrgaidphqlleakgpeaverylveeiqkvyraqgvklhdkhieivvrqmmkyvev
tdpgdsrllegqvlekwdvealnerliaegktpvawkpllmgvtksalstkswlsaasfq
ntthvlteaaiagkkdeliglkenvilgrlipagtgsdfvrftqvvdqktlkaieearke
avea

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3dxjE (E:)
maepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpna
etwamkelltgrlvfgenlvpedrlqkemeriypgeree

    Sequence, based on observed residues (ATOM records): (download) 
    >3dxjE (E:)
aepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpnae
twamkelltgrlvfgenlvpedrlqkemeriypge

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >3dxjF (F:)
mkkskrknaqaqeaqetevlvqeeaeelpefpegepdpdledpdltleddlldlpeegeg
ldleeeeedlpipkistsdpvrqylheigqvplltleeevelarkveegmeaikklseit
gldpdlirevvrakilgsarvrhipglketldpktveeidqklkslpkehkrylhiareg
eaarqhlieanlrlvvsiakkytgrglsfldliqegnqgliravekfeykrrfkfstyat
wwirqainraiadqartiripvhmvetinklsrtarqlqqelgreptyeeiaeamgpgwd
akrveetlkiaqepvsletpigdekdsfygdfipdehlpspvdaatqsllseelekalsk
lsereamvlklrkglidgrehtleevgaffgvtrerirqienkalrklkyhesrtrklrd
fld

    Sequence, based on observed residues (ATOM records): (download) 
    >3dxjF (F:)
kistsdpvrqylheigqvplltleeevelarkveegmeaikklseitgldpdlirevvra
kilgsarvrhipglketldpktveeidqklkslpkehkrylhiaregeaarqhlieanlr
lvvsiakkytgrglsfldliqegnqgliravekfeykrrfkfstyatwwirqainraiad
qartiripvhmvetinklsrtarqlqqelgreptyeeiaeamgpgwdakrveetlkiaqe
pvsletpigdekdsfygdfipdehlpspvdaatqsllseelekalsklsereamvlklrk
glidgrehtleevgaffgvtrerirqienkalrklkyhesrtrklrdfl

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    No sequence available.

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dxjM (M:)
meikrfgrireviplpplteiqvesyrralqadvppekrenvgiqaafretfpieeedkg
kgglvldfleyrlgeppfpqdecrekdltyqaplyarlqlihkdtglikedevflghipl
mtedgsfiingadrvivsqihrspgvyftpdparpgryiasiiplpkrgpwidlevepng
vvsmkvnkrkfplvlllrvlgydqetlarelgaygelvqglmdesvfamrpeealirlft
llrpgdppkrdkavayvygliadprrydlgeagrykaeeklgirlsgrtlarfedgefkd
evflptlrylfaltagvpghevddidhlgnrrirtvgelmtdqfrvglarlargvrerml
mgsedsltpaklvnsrpleaaireffsrsqlsqfkdetnplsslrhkrrisalgpggltr
eragfdvrdvhrthygricpvetpeganiglitslaayarvdelgfirtpyrrvvggvvt
devvymtateedrytiaqantplegnriaaervvarrkgepvivspeevefmdvspkqvf
svntnlipflehddanralmgsnmqtqavpliraqapvvmtgleervvrdslaalyaeed
gevakvdgnrivvryedgrlveyplrrfyrsnqgtaldqrprvvvgqrvrkgdlladgpa
sengflalgqnvlvaimpfdgynfedaiviseellkrdfytsihieryeieardtklgpe
ritrdiphlseaalrdldeegvvrigaevkpgdilvgrtsfkgeseptpeerllrsifge
kardvkdtslrvppgeggivvrtvrlrrgdpgvelkpgvrevvrvyvaqkrklqvgdkla
nrhgnkgvvakilpvedmphlpdgtpvdvilnplgvpsrmnlgqilethlglagyflgqr
yispifdgakepeikellaqafevyfgkrkgegfgvdkrevevlrraeklglvtpgktpe
eqlkelflqgkvvlydgrtgepiegpivvgqmfimklyhmvedkmharstgpyslitqqp
lggkaqfggqrfgemevwaleaygaahtlqemltlksddiegrnaayeaiikgedvpeps
vpesfrvlvkelqalaldvqtldekdnpvdifeglaskr

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >3dxjN (N:)
mkkevrkvrialaspekirswsygevekpetinyrtlkperdglfderifgpikdyecac
gkykrqrfegkvcercgvevtksivrryrmghielatpaahiwfvkdvpskigtlldlsa
teleqvlyfskyivldpkgailngvpvekrqlltdeeyrelrygkqetyplppgvdalvk
dgeevvkgqelapgvvsrldgvalyrfprrvrveyvkkeraglrlplaawvekeaykpge
ilaelpepylfraeeegvvelkeleegaflvlrredepvatyflpvgmtplvvhgeivek
gqplaeakgllrmprqvraaqveaeeegetvyltlflewtepkdyrvqphmnvvvpegar
veagdkivaaidpeeeviaeaegvvhlhepasilvvkarvypfeddvevstgdrvapgdv
ladggkvksdvygrvevdlvrnvvrvvesydidarmgaeaiqqllkeldlealekellee
mkhpsrarrakarkrlevvrafldsgnrpewmileavpvlppdlrpmvqvdggrfatsdl
ndlyrrlinrnnrlkkllaqgapeiiirnekrmlqeavdalldngrrgapvtnpgsdrpl
rsltdilsgkqgrfrqnllgkrvdysgrsvivvgpqlklhqcglpkrmalelfkpfllkk
meekgiapnvkaarrmlerqrdikdevwdaleevihgkvvllnraptlhrlgiqafqpvl
vegqsiqlhplvceafnadfdgdqmavhvplssfaqaeariqmlsahnllspasgeplak
psrdiilglyyitqvrkekkgaglefatpeealaahergevalnapikvagretsvgrlk
yvfanpdeallavahgivdlqdvvtvrymgkrletspgrilfarivaeavedekvaweli
qldvpqeknslkdlvyqaflrlgmektarlldalkyygftfsttsgitigiddavipeek
kqyleeadrkllqieqayemgfltdrerydqilqlwtettekvtqavfknfeenypfnpl
yvmaqsgargnpqqirqlcglrglmqkpsgetfevpvrssfregltvleyfisshgarkg
gadtalrtadsgyltrklvdvtheivvreadcgttnyisvplfqpdevtrslrlrkradi
eaglygrvlarevevlgvrleegrylsmddvhllikaaeageiqevpvrspltcqtrygv
cqkcygydlsmarpvsigeavgivaaqsigepgtqltmrtfhtggvagaaditqglprvi
elfearrpkakaviseidgvvrieeteeklsvfvesegfskeyklpkearllvkdgdyve
agqpltrgaidphqlleakgpeaverylveeiqkvyraqgvklhdkhieivvrqmmkyve
vtdpgdsrllegqvlekwdvealnerliaegktpvawkpllmgvtksalstkswlsaasf
qntthvlteaaiagkkdeliglkenvilgrlipagtgsdfvrftqvvdqktlkaieeark
eaveakerpaarrgvkreqpgkqa

    Sequence, based on observed residues (ATOM records): (download) 
    >3dxjN (N:)
kkevrkvrialaspekirswsygevekpetinyrtlkperdglfderifgpikdyecacg
kykrqrfegkvcercgvevtksivrryrmghielatpaahiwfvkdvpskigtlldlsat
eleqvlyfskyivldpkgailngvpvekrqlltdeeyrelrygkqetyplppgvdalvkd
geevvkgqelapgvvsrldgvalyrfprrvrveyvkkeraglrlplaawvekeaykpgei
laelpepylfraeeegvvelkeleegaflvlrredepvatyflpvgmtplvvhgeivekg
qplaeakgllrmprqvraaqveaeeegetvyltlflewtepkdyrvqphmnvvvpegarv
eagdkivaaidpeeeviaeaegvvhlhepasilvvkarvypfeddvevstgdrvapgdvl
adggkvksdvygrvevdlvrnvvrvvesydidarmgaeaiqqllkeldlealekelleem
khpsrarrakarkrlevvrafldsgnrpewmileavpvlppdlrpmvqvdggrfatsdln
dlyrrlinrnnrlkkllaqgapeiiirnekrmlqeavdalldngrrgapvtnpgsdrplr
sltdilsgkqgrfrqnllgkrvdysgrsvivvgpqlklhqcglpkrmalelfkpfllkkm
eekgiapnvkaarrmlerqrdikdevwdaleevihgkvvllnraptlhrlgiqafqpvlv
egqsiqlhplvceafnadfdgdqmavhvplssfaqaeariqmlsahnllspasgeplakp
srdiilglyyitqvrkekkgaglefatpeealaahergevalnapikvagretsvgrlky
vfanpdeallavahgivdlqdvvtvrymgkrletspgrilfarivaeavedekvaweliq
ldvpqeknslkdlvyqaflrlgmektarlldalkyygftfsttsgitigiddavipeekk
qyleeadrkllqieqayemgfltdrerydqilqlwtettekvtqavfknfeenypfnply
vmaqsgargnpqqirqlcglrglmqkpsgetfevpvrssfregltvleyfisshgarkgg
adtalrtadsgyltrklvdvtheivvreadcgttnyisvplfqpdevtrslrlrkradie
aglygrvlarevevlgvrleegrylsmddvhllikaaeageiqevpvrspltcqtrygvc
qkcygydlsmarpvsigeavgivaaqsigepgtqltmrtfhtggvagaaditqglprvie
lfearrpkakaviseidgvvrieeteeklsvfvesegfskeyklpkearllvkdgdyvea
gqpltrgaidphqlleakgpeaverylveeiqkvyraqgvklhdkhieivvrqmmkyvev
tdpgdsrllegqvlekwdvealnerliaegktpvawkpllmgvtksalstkswlsaasfq
ntthvlteaaiagkkdeliglkenvilgrlipagtgsdfvrftqvvdqktlkaieearke
avea

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >3dxjO (O:)
maepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpna
etwamkelltgrlvfgenlvpedrlqkemeriypgeree

    Sequence, based on observed residues (ATOM records): (download) 
    >3dxjO (O:)
aepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpnae
twamkelltgrlvfgenlvpedrlqkemeriypge

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >3dxjP (P:)
mkkskrknaqaqeaqetevlvqeeaeelpefpegepdpdledpdltleddlldlpeegeg
ldleeeeedlpipkistsdpvrqylheigqvplltleeevelarkveegmeaikklseit
gldpdlirevvrakilgsarvrhipglketldpktveeidqklkslpkehkrylhiareg
eaarqhlieanlrlvvsiakkytgrglsfldliqegnqgliravekfeykrrfkfstyat
wwirqainraiadqartiripvhmvetinklsrtarqlqqelgreptyeeiaeamgpgwd
akrveetlkiaqepvsletpigdekdsfygdfipdehlpspvdaatqsllseelekalsk
lsereamvlklrkglidgrehtleevgaffgvtrerirqienkalrklkyhesrtrklrd
fld

    Sequence, based on observed residues (ATOM records): (download) 
    >3dxjP (P:)
kistsdpvrqylheigqvplltleeevelarkveegmeaikklseitgldpdlirevvra
kilgsarvrhipglketldpktveeidqklkslpkehkrylhiaregeaarqhlieanlr
lvvsiakkytgrglsfldliqegnqgliravekfeykrrfkfstyatwwirqainraiad
qartiripvhmvetinklsrtarqlqqelgreptyeeiaeamgpgwdakrveetlkiaqe
pvsletpigdekdsfygdfipdehlpspvdaatqsllseelekalsklsereamvlklrk
glidgrehtleevgaffgvtrerirqienkalrklkyhesrtrklrdfl