1HQMD

Crystal structure of thermus aquaticus core rna polymerase-includes complete structure with side-chains (except for disordered regions)-further refined from original deposition-contains additional sequence information
Total Genus 180
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
180
sequence length
1235
structure length
1175
Chain Sequence
KEVRKVRIALASPEKIRSWSYGEVEKPETEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFATELEQVLYFNKYIVLDPKGAVLDGVPVEKRQLLTDXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIDARMGAEAIQELLKELDLEKLERELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGLLDLQDTVTTRYLGRRLETNPGRILFARIVGEAVGDEKVAQELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVREADCGTTKYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTGTDITQGLPRVIELFEARRPKAKAVISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSPLLEGQVLEKWDVEALNERLIAVPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQRTLKAIE
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

publication title Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly.
pubmed doi rcsb
molecule tags Transferase
molecule keywords DNA-directed RNA polymerase subunit alpha
total genus 180
structure length 1175
sequence length 1235
ec nomenclature ec 2.7.7.6: DNA-directed RNA polymerase.
pdb deposition date 2000-12-18

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D PF00623 RNA_pol_Rpb1_2 RNA polymerase Rpb1, domain 2
D PF04983 RNA_pol_Rpb1_3 RNA polymerase Rpb1, domain 3
D PF04998 RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5
D PF05000 RNA_pol_Rpb1_4 RNA polymerase Rpb1, domain 4
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.132.30 Mainly Alpha Orthogonal Bundle Topoisomerase I; Chain A, domain 4 Topoisomerase I; Chain A, domain 4 1hqmD03
1.10.274.100 Mainly Alpha Orthogonal Bundle Enzyme I; Chain A, domain 2 Enzyme I; Chain A, domain 2 1hqmD02
3.90.105.30 Alpha Beta Alpha-Beta Complex Molybdopterin biosynthesis moea protein, domain 2 Molybdopterin biosynthesis moea protein, domain 2 1hqmD05
3GTOA 2WAQA 1YNJD 2BE5D 2E2IA 4QIWA 1SFOA 1I3QA 1SMYD 2NVYA 1IW7D 1TWHA 1TWFA 2A69D 3HKZA 3GTQA 2R93A 2O5JD 2E2HA 3FKIA 2R7ZA 2B63A 2JA7A 2WB1A 2Y0SA 1K83A 3GTMA 2YU9A 2VUMA 1ZYRD 3CQZA 1TWCA 3GTLA 3GTJA 2A6ED 2JA5A 1I50A 3GTPA 1HQMD 1WCMA 2A68D 2JA6A 3H0GA 1R9TA 3GTKA 2A6HD 2PMZA 1TWAA 1YNND 1TWGA 1Y1VA 2R92A 3GTGA 2CW0D 4C2MA 2NVXA 1I6VD 4AYBA 1Y1WA
chains in the Genus database with same CATH superfamily
3GTOA 1YNJD 2BE5D 4QCLA 4BAAA 1T8IA 2MP0A 1I3QA 2NVYA 1TWHA 1A36A 5JSNB 3K5LA 3U44A 2JA7A 1UZ5A 2FIPA 4BABA 2NQSA 1Y2MA 2EZAA 2NRPA 2R4GA 4D3ZA 3GTMA 2YU9A 1EH1A 3MAQA 2NROA 1ZYRD 3GTJA 1K4SA 1WQFA 4CEHA 4U91A 5G2RA 3GTPA 1T6PA 1SEUA 1EJ9A 2EZCA 1EK8A 5JSBB 3DU5A 3K59A 4NWBA 2B9SB 1TWAA 4FXDA 5ERRA 5C9HA 4KC6A 2K3OA 5IZ2A 3GTGA 2X3LA 1DD5A 1NH3A 4LMOA 2LPJA 3LF9A 5CQGA 1T6JA 2N1DB 1RRJA 2E2IA 4QIWA 4U90A 1SMYD 3K58A 1TWFA 2A69D 2VK9A 2R7ZA 4IP8A 2E2HA 2MX8A 3P9AA 1LPQA 2NQUA 4EJ3A 2NQVA 1K4TA 2A6ED 2NQKA 3LR6A 2NQRA 4Q5GA 1MIUA 3EZAA 1G8LA 4TK3A 1WCMA 1WQGA 2A68D 4KB4A 4FYDA 1T3EA 2X0PA 3H0GA 1R9TA 2N3EA 1A31A 2NQQA 5ERSA 4V2RA 1YNND 5ERUA 1G8RA 2AQLA 2YIIA 3IAYA 3LR2A 3K5MA 3JSYA 4H3TA 4L8IA 4C2MA 2NVXA 4C5RA 1XI8A 2Y0NA 1EZAA 4PD0A 2WAQA 4KAWX 4KB2A 4OYDB 4TK1A 2FTSA 1IW7D 5ERQA 5MLC9 3EZEA 3K57A 1IS1A 2Y0SA 4NOMA 1K83A 4D3YA 4C5SA 3CQZA 1TWCA 2EZBA 2HWGA 4FBSA 5G2SA 1I50A 4C6GA 1HQMD 4AN8A 2NQNA 1TL8A 2K3NA 3EZBA 4GFQA 3LRDA 1V9MA 3GTKA 2A6HD 4AHCA 1ZYMA 5ERVA 2R92A 2K3QA 1A35A 1ISEA 4CEIA 2FIOA 4AYBA 1RR8C 1FC5A 2HROA 4NOKA 4FGUA 3K5OA 1WU2A 5ERTA 4F3EA 5D6GA 1WQHA 1Q8IA 4O26A 1SFOA 2R93A 3HKZA 3M4AA 1SC7A 4Q5VA 3GTQA 2O5JD 2B63A 2LTHA 3FKIA 3NZ4A 4C5UA 2NRSA 2WB1A 4V2QA 2VUMA 1GE9A 4CQ5A 2FU3A 2NQMA 4IP9A 3SJRA 3K5NA 4CEJA 3GTLA 3U4QA 4NOLA 2JA5A 4PD1A 1TGOA 3DU6A 4KDDA 3LHPS 1R5ZA 2LKMB 2LYIA 5D8HB 2JA6A 2F5JA 2X0OA 2X0QA 1EZBA 1Y698 2LPIA 1W27A 4JLRC 2PMZA 2F4QA 2MX9A 1TWGA 1Y1VA 2CW0D 3WVOA 1I6VD 1R49A 1Y1WA 2MQAA 3LR8A 4TK4A 3KYLA
chains in the Genus database with same CATH topology
3GTOA 1YNJD 2BE5D 4QCLA 1T8IA 1I3QA 2NVYA 1TWHA 1A36A 5JSNB 3K5LA 3U44A 2JA7A 1UZ5A 2FIPA 2NRPA 2NQSA 2R4GA 4D3ZA 3GTMA 2YU9A 1EH1A 3MAQA 2NROA 1ZYRD 3GTJA 1K4SA 1WQFA 4CEHA 4U91A 5G2RA 3GTPA 1SEUA 1EJ9A 1EK8A 5JSBB 3DU5A 3K59A 4NWBA 2B9SB 1TWAA 4FXDA 5ERRA 5C9HA 4KC6A 2K3OA 5IZ2A 3GTGA 2X3LA 1DD5A 1NH3A 4LMOA 2LPJA 3LF9A 5CQGA 2N1DB 1RRJA 2E2IA 4QIWA 4U90A 1SMYD 3K58A 1TWFA 2A69D 2VK9A 2R7ZA 4IP8A 2E2HA 2MX8A 3P9AA 1LPQA 2NQUA 4EJ3A 2NQVA 1K4TA 2A6ED 2NQKA 3LR6A 2NQRA 4Q5GA 1MIUA 1G8LA 4TK3A 1WCMA 1WQGA 2A68D 4KB4A 4FYDA 1T3EA 2X0PA 3H0GA 1R9TA 2N3EA 1A31A 2NQQA 5ERSA 1YNND 5ERUA 1G8RA 2AQLA 3IAYA 3LR2A 3K5MA 3JSYA 4H3TA 4L8IA 4C2MA 2NVXA 1XI8A 2Y0NA 4PD0A 2WAQA 4KAWX 4KB2A 4OYDB 4TK1A 2FTSA 1IW7D 5ERQA 5MLC9 3K57A 1IS1A 2Y0SA 4NOMA 1K83A 4D3YA 3CQZA 1TWCA 4FBSA 5G2SA 1I50A 1HQMD 4AN8A 2NQNA 1TL8A 2K3NA 4GFQA 3LRDA 1V9MA 3GTKA 2A6HD 4AHCA 5ERVA 2R92A 2K3QA 1A35A 1ISEA 4CEIA 2FIOA 4AYBA 1RR8C 1FC5A 1WU2A 4NOKA 4FGUA 3K5OA 5ERTA 4F3EA 5D6GA 1WQHA 1Q8IA 4O26A 1SFOA 2R93A 3HKZA 3M4AA 1SC7A 4Q5VA 3GTQA 2O5JD 2B63A 2LTHA 3FKIA 2NRSA 2WB1A 2VUMA 1GE9A 2FU3A 2NQMA 4IP9A 3SJRA 3K5NA 4CEJA 3GTLA 3U4QA 4NOLA 2JA5A 4PD1A 1TGOA 3DU6A 4KDDA 3LHPS 1R5ZA 2LKMB 2LYIA 5D8HB 2JA6A 2F5JA 2X0OA 2X0QA 1Y698 2LPIA 4JLRC 2PMZA 2F4QA 2MX9A 1TWGA 1Y1VA 2CW0D 3WVOA 1I6VD 1R49A 1Y1WA 2MQAA 3LR8A 4TK4A 3KYLA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3GTO A;  2WAQ A;  1YNJ D;  2BE5 D;  2E2I A;  4QIW A;  1SFO A;  1I3Q A;  1SMY D;  2NVY A;  1IW7 D;  1TWH A;  1TWF A;  2A69 D;  3HKZ A;  3GTQ A;  2R93 A;  2O5J D;  2E2H A;  3FKI A;  2R7Z A;  2B63 A;  2JA7 A;  2WB1 A;  2Y0S A;  1K83 A;  3GTM A;  2YU9 A;  2VUM A;  1ZYR D;  3CQZ A;  1TWC A;  3GTL A;  3GTJ A;  2A6E D;  2JA5 A;  1I50 A;  3GTP A;  1HQM D;  1WCM A;  2A68 D;  2JA6 A;  3H0G A;  1R9T A;  3GTK A;  2A6H D;  2PMZ A;  1TWA A;  1YNN D;  1TWG A;  1Y1V A;  2R92 A;  3GTG A;  2CW0 D;  4C2M A;  2NVX A;  1I6V D;  4AYB A;  1Y1W A; 
#chains in the Genus database with same CATH topology
 3GTO A;  1YNJ D;  2BE5 D;  4QCL A;  4BAA A;  1T8I A;  2MP0 A;  1I3Q A;  2NVY A;  1TWH A;  1A36 A;  5JSN B;  3K5L A;  3U44 A;  2JA7 A;  1UZ5 A;  2FIP A;  4BAB A;  2NQS A;  1Y2M A;  2EZA A;  2NRP A;  2R4G A;  4D3Z A;  3GTM A;  2YU9 A;  1EH1 A;  3MAQ A;  2NRO A;  1ZYR D;  3GTJ A;  1K4S A;  1WQF A;  4CEH A;  4U91 A;  5G2R A;  3GTP A;  1T6P A;  1SEU A;  1EJ9 A;  2EZC A;  1EK8 A;  5JSB B;  3DU5 A;  3K59 A;  4NWB A;  2B9S B;  1TWA A;  4FXD A;  5ERR A;  5C9H A;  4KC6 A;  2K3O A;  5IZ2 A;  3GTG A;  2X3L A;  1DD5 A;  1NH3 A;  4LMO A;  2LPJ A;  3LF9 A;  5CQG A;  1T6J A;  2N1D B;  1RRJ A;  2E2I A;  4QIW A;  4U90 A;  1SMY D;  3K58 A;  1TWF A;  2A69 D;  2VK9 A;  2R7Z A;  4IP8 A;  2E2H A;  2MX8 A;  3P9A A;  1LPQ A;  2NQU A;  4EJ3 A;  2NQV A;  1K4T A;  2A6E D;  2NQK A;  3LR6 A;  2NQR A;  4Q5G A;  1MIU A;  3EZA A;  1G8L A;  4TK3 A;  1WCM A;  1WQG A;  2A68 D;  4KB4 A;  4FYD A;  1T3E A;  2X0P A;  3H0G A;  1R9T A;  2N3E A;  1A31 A;  2NQQ A;  5ERS A;  4V2R A;  1YNN D;  5ERU A;  1G8R A;  2AQL A;  2YII A;  3IAY A;  3LR2 A;  3K5M A;  3JSY A;  4H3T A;  4L8I A;  4C2M A;  2NVX A;  4C5R A;  1XI8 A;  2Y0N A;  1EZA A;  4PD0 A;  2WAQ A;  4KAW X;  4KB2 A;  4OYD B;  4TK1 A;  2FTS A;  1IW7 D;  5ERQ A;  5MLC 9;  3EZE A;  3K57 A;  1IS1 A;  2Y0S A;  4NOM A;  1K83 A;  4D3Y A;  4C5S A;  3CQZ A;  1TWC A;  2EZB A;  2HWG A;  4FBS A;  5G2S A;  1I50 A;  4C6G A;  1HQM D;  4AN8 A;  2NQN A;  1TL8 A;  2K3N A;  3EZB A;  4GFQ A;  3LRD A;  1V9M A;  3GTK A;  2A6H D;  4AHC A;  1ZYM A;  5ERV A;  2R92 A;  2K3Q A;  1A35 A;  1ISE A;  4CEI A;  2FIO A;  4AYB A;  1RR8 C;  1FC5 A;  2HRO A;  4NOK A;  4FGU A;  3K5O A;  1WU2 A;  5ERT A;  4F3E A;  5D6G A;  1WQH A;  1Q8I A;  4O26 A;  1SFO A;  2R93 A;  3HKZ A;  3M4A A;  1SC7 A;  4Q5V A;  3GTQ A;  2O5J D;  2B63 A;  2LTH A;  3FKI A;  3NZ4 A;  4C5U A;  2NRS A;  2WB1 A;  4V2Q A;  2VUM A;  1GE9 A;  4CQ5 A;  2FU3 A;  2NQM A;  4IP9 A;  3SJR A;  3K5N A;  4CEJ A;  3GTL A;  3U4Q A;  4NOL A;  2JA5 A;  4PD1 A;  1TGO A;  3DU6 A;  4KDD A;  3LHP S;  1R5Z A;  2LKM B;  2LYI A;  5D8H B;  2JA6 A;  2F5J A;  2X0O A;  2X0Q A;  1EZB A;  1Y69 8;  2LPI A;  1W27 A;  4JLR C;  2PMZ A;  2F4Q A;  2MX9 A;  1TWG A;  1Y1V A;  2CW0 D;  3WVO A;  1I6V D;  1R49 A;  1Y1W A;  2MQA A;  3LR8 A;  4TK4 A;  3KYL A; 
#chains in the Genus database with same CATH homology
 3GTO A;  1YNJ D;  2BE5 D;  4QCL A;  1T8I A;  1I3Q A;  2NVY A;  1TWH A;  1A36 A;  5JSN B;  3K5L A;  3U44 A;  2JA7 A;  1UZ5 A;  2FIP A;  2NRP A;  2NQS A;  2R4G A;  4D3Z A;  3GTM A;  2YU9 A;  1EH1 A;  3MAQ A;  2NRO A;  1ZYR D;  3GTJ A;  1K4S A;  1WQF A;  4CEH A;  4U91 A;  5G2R A;  3GTP A;  1SEU A;  1EJ9 A;  1EK8 A;  5JSB B;  3DU5 A;  3K59 A;  4NWB A;  2B9S B;  1TWA A;  4FXD A;  5ERR A;  5C9H A;  4KC6 A;  2K3O A;  5IZ2 A;  3GTG A;  2X3L A;  1DD5 A;  1NH3 A;  4LMO A;  2LPJ A;  3LF9 A;  5CQG A;  2N1D B;  1RRJ A;  2E2I A;  4QIW A;  4U90 A;  1SMY D;  3K58 A;  1TWF A;  2A69 D;  2VK9 A;  2R7Z A;  4IP8 A;  2E2H A;  2MX8 A;  3P9A A;  1LPQ A;  2NQU A;  4EJ3 A;  2NQV A;  1K4T A;  2A6E D;  2NQK A;  3LR6 A;  2NQR A;  4Q5G A;  1MIU A;  1G8L A;  4TK3 A;  1WCM A;  1WQG A;  2A68 D;  4KB4 A;  4FYD A;  1T3E A;  2X0P A;  3H0G A;  1R9T A;  2N3E A;  1A31 A;  2NQQ A;  5ERS A;  1YNN D;  5ERU A;  1G8R A;  2AQL A;  3IAY A;  3LR2 A;  3K5M A;  3JSY A;  4H3T A;  4L8I A;  4C2M A;  2NVX A;  1XI8 A;  2Y0N A;  4PD0 A;  2WAQ A;  4KAW X;  4KB2 A;  4OYD B;  4TK1 A;  2FTS A;  1IW7 D;  5ERQ A;  5MLC 9;  3K57 A;  1IS1 A;  2Y0S A;  4NOM A;  1K83 A;  4D3Y A;  3CQZ A;  1TWC A;  4FBS A;  5G2S A;  1I50 A;  1HQM D;  4AN8 A;  2NQN A;  1TL8 A;  2K3N A;  4GFQ A;  3LRD A;  1V9M A;  3GTK A;  2A6H D;  4AHC A;  5ERV A;  2R92 A;  2K3Q A;  1A35 A;  1ISE A;  4CEI A;  2FIO A;  4AYB A;  1RR8 C;  1FC5 A;  1WU2 A;  4NOK A;  4FGU A;  3K5O A;  5ERT A;  4F3E A;  5D6G A;  1WQH A;  1Q8I A;  4O26 A;  1SFO A;  2R93 A;  3HKZ A;  3M4A A;  1SC7 A;  4Q5V A;  3GTQ A;  2O5J D;  2B63 A;  2LTH A;  3FKI A;  2NRS A;  2WB1 A;  2VUM A;  1GE9 A;  2FU3 A;  2NQM A;  4IP9 A;  3SJR A;  3K5N A;  4CEJ A;  3GTL A;  3U4Q A;  4NOL A;  2JA5 A;  4PD1 A;  1TGO A;  3DU6 A;  4KDD A;  3LHP S;  1R5Z A;  2LKM B;  2LYI A;  5D8H B;  2JA6 A;  2F5J A;  2X0O A;  2X0Q A;  1Y69 8;  2LPI A;  4JLR C;  2PMZ A;  2F4Q A;  2MX9 A;  1TWG A;  1Y1V A;  2CW0 D;  3WVO A;  1I6V D;  1R49 A;  1Y1W A;  2MQA A;  3LR8 A;  4TK4 A;  3KYL A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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