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 2.04 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 2.04: 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 2.04: 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 2.04: 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 2.04: 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 2.04: 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 2.04: 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.