Structure of PDB 1smy Chain D

Receptor sequence
>1smyD (length=1392) Species: 274 (Thermus thermophilus) [Search protein sequence]
KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQ
LLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG
VALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLF
GDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGD
RVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQ
LLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMI
LEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAP
EIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGR
FRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEE
KGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGI
QAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQM
LSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEAL
AAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDV
VTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKD
LVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQY
LEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEE
NYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFRE
GLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCG
TTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEG
RYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMAR
PVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF
EARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLV
KDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKL
HDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKT
PVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLK
ENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEA
3D structure
PDB1smy Structural basis for transcription regulation by alarmone ppGpp
ChainD
Resolution2.7 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 ZN D C1112 C1201 C1204 C999 C1088 C1091
BS02 MG D D739 D741 D743 D626 D628 D630
BS03 MG D D739 D741 D626 D628
BS04 MG D V1371 V1372 M1375 V1258 V1259 M1262
BS05 MG D E734 S782 E621 S669
BS06 MG D R1164 D1170 R1051 D1057
BS07 MG D P509 E510 W511 M512 I513 P396 E397 W398 M399 I400
BS08 MG D S429 D430 V431 Y432 S316 D317 V318 Y319
BS09 MG D T1196 R1197 Y1198 G1199 T1083 R1084 Y1085 G1086
BS10 MG D I827 D862 V863 I714 D749 V750
BS11 MG D S1060 E1063 S947 E950
BS12 MG D K1047 P1048 K1079 K934 P935 K966
BS13 MG D L639 S765 A766 L526 S652 A653
BS14 MG D N1010 N1014 N897 N901
BS15 MG D G1218 G1475 G1105 G1362
BS16 MG D Y215 V216 H388 E389 Y214 V215 H275 E276
BS17 MG D V377 A379 V264 A266
BS18 MG D A735 F736 A622 F623
BS19 MG D H696 G697 H583 G584
BS20 MG D M869 E893 M756 E780
BS21 MG D G1064 L1065 T1066 G951 L952 T953
BS22 MG D P208 R209 P207 R208
BS23 MG D R87 Y88 L524 R86 Y87 L411
BS24 MG D V829 A830 V716 A717
BS25 MG D T1004 R1036 T891 R923
BS26 MG D R399 S429 D430 Y432 R286 S316 D317 Y319
BS27 MG D D953 P1019 D840 P906
BS28 MG D T1382 A1416 W1417 K1418 T1269 A1303 W1304 K1305
BS29 MG D P39 D46 E47 P38 D45 E46
BS30 MG D L223 R224 G364 D365 L222 R223 G251 D252
BS31 MG D N33 Y34 R35 N32 Y33 R34
BS32 MG D G70 E79 G69 E78
BS33 MG D V1400 E1401 V1287 E1288
BS34 MG D K800 A802 L804 V829 K687 A689 L691 V716
BS35 MG D D892 E893 D779 E780
BS36 MG D D1111 R1189 D998 R1076
BS37 MG D D117 L118 D116 L117
BS38 MG D E1497 K1500 E1501 E1384 K1387 E1388
BS39 MG D K149 R150 K148 R149
BS40 MG D F1299 S1300 F1186 S1187
BS41 MG D Y401 V415 A416 Y288 V302 A303
BS42 MG D D107 R586 D106 R473
BS43 MG D K960 S1059 K847 S946
BS44 MG D Y868 M869 Y755 M756
BS45 MG D K62 Y63 E74 K61 Y62 E73
BS46 MG D R1087 T1234 R974 T1121
BS47 MG D D55 Y56 K82 D54 Y55 K81
BS48 MG D F68 G70 K71 F67 G69 K70
BS49 MG D M512 I513 M399 I400
BS50 MG D E219 R220 A221 E218 R219 A220
BS51 MG D W897 L902 W784 L789
BS52 MG D K131 R572 K130 R459
BS53 G4P D N737 R783 E1231 Q1235 N624 R670 E1118 Q1122
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:1smy, PDBe:1smy, PDBj:1smy
PDBsum1smy
PubMed15109491
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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