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.

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


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