PDB entry 2ppb

View 2ppb on RCSB PDB site
Description: Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin
Class: transferase/DNA/RNA
Keywords: RNA polymerase, elongation complex, template DNA, non-template DNA, RNA transcript, NTP substrate, antibiotic streptolydigin, transferase-DNA-RNA complex
Deposited on 2007-04-28, released 2007-07-17
The last revision prior to the SCOPe 2.08 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.234
AEROSPACI score: 0.16 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA-directed RNA polymerase alpha chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: DNA-directed RNA polymerase alpha chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: DNA-directed RNA polymerase beta chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2ppbc_
  • Chain 'D':
    Compound: DNA-directed RNA polymerase beta' chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2ppbd_
  • Chain 'E':
    Compound: DNA-directed RNA polymerase omega chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2ppbe_
  • Chain 'G':
    Compound: DNA (5'-d(p*cp*cp*cp*tp*gp*tp*cp*tp*gp*gp*cp*gp*tp*tp*cp*gp*cp*gp*cp*gp*cp*cp*g)-3')
  • Chain 'H':
    Compound: RNA (5'-r(p*gp*ap*gp*up*cp*up*gp*cp*gp*gp*cp*gp*cp*gp*cp*g)-3')
  • Chain 'I':
    Compound: DNA (5'-d(*ap*ap*cp*gp*cp*cp*ap*gp*ap*cp*ap*gp*gp*g)-3')
  • Chain 'K':
    Compound: DNA-directed RNA polymerase alpha chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: DNA-directed RNA polymerase alpha chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: DNA-directed RNA polymerase beta chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2ppbm_
  • Chain 'N':
    Compound: DNA-directed RNA polymerase beta' chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2ppbn_
  • Chain 'O':
    Compound: DNA-directed RNA polymerase omega chain
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2ppbo_
  • Chain 'X':
    Compound: DNA (5'-d(p*cp*cp*cp*tp*gp*tp*cp*tp*gp*gp*cp*gp*tp*tp*cp*gp*cp*gp*cp*gp*cp*cp*g)-3')
  • Chain 'Y':
    Compound: RNA (5'-r(p*gp*ap*gp*up*cp*up*gp*cp*gp*gp*cp*gp*cp*gp*cp*g)-3')
  • Chain 'Z':
    Compound: DNA (5'-d(*ap*ap*cp*gp*cp*cp*ap*gp*ap*cp*ap*gp*gp*g)-3')
  • Heterogens: STD, ZN, MG, APC, 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) 
    >2ppbC (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) 
    >2ppbD (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) 
    >2ppbD (D:)
kkevrkvrialaspekirswsygevekpetinyrtlkperdglfderifgpikdyecacg
kykrqrfegkvcercgvevtksivrryrmghielatpaahiwfvkdvpskigtlldlsat
eleqvlyfskyivldpkgailngvpvekrqlltdeeyrelrygkqetyplppgvdalvkd
geevvkgqelapgvvsrldgvalyrfasilvvkarvypfeddvevstgdrvapgdvladg
gkvksdvygrvevdlvrnvvrvvesydidarmgaeaiqqllkeldlealekelleemkhp
srarrakarkrlevvrafldsgnrpewmileavpvlppdlrpmvqvdggrfatsdlndly
rrlinrnnrlkkllaqgapeiiirnekrmlqeavdalldngrrgapvtnpgsdrplrslt
dilsgkqgrfrqnllgkrvdysgrsvivvgpqlklhqcglpkrmalelfkpfllkkmeek
giapnvkaarrmlerqrdikdevwdaleevihgkvvllnraptlhrlgiqafqpvlvegq
siqlhplvceafnadfdgdqmavhvplssfaqaeariqmlsahnllspasgeplakpsrd
iilglyyitqvrkekkgaglefatpeealaahergevalnapikvagretsvgrlkyvfa
npdeallavahgivdlqdvvtvrymgkrletspgrilfarivaeavedekvaweliqldv
pqeknslkdlvyqaflrlgmektarlldalkyygftfsttsgitigiddavipeekkqyl
eeadrkllqieqayemgfltdrerydqilqlwtettekvtqavfknfeenypfnplyvma
qsgargnpqqirqlcglrglmqkpsgetfevpvrssfregltvleyfisshgarkggadt
alrtadsgyltrklvdvtheivvreadcgttnyisvplfqpdevtrslrlrkradieagl
ygrvlarevevlgvrleegrylsmddvhllikaaeageiqevpvrspltcqtrygvcqkc
ygydlsmarpvsigeavgivaaqsigepgtqltmrtfhtditqglprvielfearrpkak
aviseidgvvrieeteeklsvfvesegfskeyklpkearllvkdgdyveagqpltrgaid
phqlleakgpeaverylveeiqkvyraqgvklhdkhieivvrqmmkyvevtdpgdsrlle
gqvlekwdvealnerliaegktpvawkpllmgvtksalstkswlsaasfqntthvlteaa
iagkkdeliglkenvilgrlipagtgsdfvrftqvvdqktlkaieearkeavea

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >2ppbE (E:)
maepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpna
vtwamkelltgrlvfgenlvpedrlqkemerlypveree

    Sequence, based on observed residues (ATOM records): (download) 
    >2ppbE (E:)
aepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpnav
twamkelltgrlvfgenlvpedrlqkemerlypve

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    No sequence available.

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ppbM (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) 
    >2ppbN (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) 
    >2ppbN (N:)
kkevrkvrialaspekirswsygevekpetinyrtlkperdglfderifgpikdyecacg
kykrqrfegkvcercgvevtksivrryrmghielatpaahiwfvkdvpskigtlldlsat
eleqvlyfskyivldpkgailngvpvekrqlltdeeyrelrygkqetyplppgvdalvkd
geevvkgqelapgvvsrldgvalyrfasilvvkarvypfeddvevstgdrvapgdvladg
gkvksdvygrvevdlvrnvvrvvesydidarmgaeaiqqllkeldlealekelleemkhp
srarrakarkrlevvrafldsgnrpewmileavpvlppdlrpmvqvdggrfatsdlndly
rrlinrnnrlkkllaqgapeiiirnekrmlqeavdalldngrrgapvtnpgsdrplrslt
dilsgkqgrfrqnllgkrvdysgrsvivvgpqlklhqcglpkrmalelfkpfllkkmeek
giapnvkaarrmlerqrdikdevwdaleevihgkvvllnraptlhrlgiqafqpvlvegq
siqlhplvceafnadfdgdqmavhvplssfaqaeariqmlsahnllspasgeplakpsrd
iilglyyitqvrkekkgaglefatpeealaahergevalnapikvagretsvgrlkyvfa
npdeallavahgivdlqdvvtvrymgkrletspgrilfarivaeavedekvaweliqldv
pqeknslkdlvyqaflrlgmektarlldalkyygftfsttsgitigiddavipeekkqyl
eeadrkllqieqayemgfltdrerydqilqlwtettekvtqavfknfeenypfnplyvma
qsgargnpqqirqlcglrglmqkpsgetfevpvrssfregltvleyfisshgarkggadt
alrtadsgyltrklvdvtheivvreadcgttnyisvplfqpdevtrslrlrkradieagl
ygrvlarevevlgvrleegrylsmddvhllikaaeageiqevpvrspltcqtrygvcqkc
ygydlsmarpvsigeavgivaaqsigepgtqltmrtfhtditqglprvielfearrpkak
aviseidgvvrieeteeklsvfvesegfskeyklpkearllvkdgdyveagqpltrgaid
phqlleakgpeaverylveeiqkvyraqgvklhdkhieivvrqmmkyvevtdpgdsrlle
gqvlekwdvealnerliaegktpvawkpllmgvtksalstkswlsaasfqntthvlteaa
iagkkdeliglkenvilgrlipagtgsdfvrftqvvdqktlkaieearkeavea

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >2ppbO (O:)
maepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpna
vtwamkelltgrlvfgenlvpedrlqkemerlypveree

    Sequence, based on observed residues (ATOM records): (download) 
    >2ppbO (O:)
aepgidklfgmvdskyrltvvvakraqqllrhgfkntvlepeerpkmqtleglfddpnav
twamkelltgrlvfgenlvpedrlqkemerlypve

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    No sequence available.