Structure of PDB 3dxj Chain D

Receptor sequence
>3dxjD (length=1504) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]
KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQ
LLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG
VALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLF
RAEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKG
QPLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHM
NVVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVY
PFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYD
IDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRA
FLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRN
NRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLR
SLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALE
LFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVL
LNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPL
SSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKG
AGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALL
AVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQ
LDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGI
DDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTE
KVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGE
TFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDV
THEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAR
EVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVC
QKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAAD
ITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSK
EYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEE
IQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVE
ALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAA
IAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKE
AVEA
3D structure
PDB3dxj The RNA polymerase "switch region" is a target for inhibitors.
ChainD
Resolution3.0 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 MG D K840 V842 K839 V841
BS02 ZN D C58 K62 C73 C57 K61 C72
BS03 ZN D C1112 C1194 C1204 C1111 C1193 C1203
BS04 MG D D739 D741 D743 D738 D740 D742
BS05 NE6 D F614 L619 G620 V1099 H1103 A1438 S1439 K1463 I1467 F613 L618 G619 V1098 H1102 A1437 S1438 K1462 I1466 PDBbind-CN: -logKd/Ki=6.22,Kd=0.6uM
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dxj, PDBe:3dxj, PDBj:3dxj
PDBsum3dxj
PubMed18957204
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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