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
b'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.

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


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