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 |
40
|
sequence length |
266
|
structure length |
266
|
Chain Sequence |
EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD
|
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.
After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.
| publication title |
Mechanism of transcriptional stalling at cisplatin-damaged DNA.
pubmed doi rcsb |
| molecule keywords |
5'-D(*TP*AP*CP*TP*TP*GUP*CP*CP*CP*TP*CP*CP*TP*CP*AP*T)-3'
|
| molecule tags |
Transcription/dna-rna hybrid
|
| total genus |
40
|
| structure length |
266
|
| sequence length |
266
|
| ec nomenclature | |
| pdb deposition date | 2007-09-10 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| C | PF01000 | RNA_pol_A_bac | RNA polymerase Rpb3/RpoA insert domain |
| C | PF01193 | RNA_pol_L | RNA polymerase Rpb3/Rpb11 dimerisation domain |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Mainly Beta | Beta Complex | RNA Polymerase Alpha Subunit; Chain A, domain 2 | DNA-directed RNA polymerase, insert domain | ||
| Alpha Beta | 2-Layer Sandwich | Gyrase A; domain 2 | RNA polymerase, RBP11-like subunit |
#chains in the Genus database with same CATH superfamily 2R7Z C; 1TWF K; 4G7H A; 4A3F C; 2R7Z K; 1SMY A; 4A3F K; 1WCM C; 4XLN A; 1WCM K; 4OIQ A; 1XPP A; 3H0G C; 4QJV A; 1I6V A; 3CQZ C; 4JK1 A; 4A3C C; 4QJV B; 4C3J C; 3H0G K; 2O5J A; 3CQZ K; 4A3C K; 5M5W K; 4C3J K; 4YG2 A; 5IP7 C; 3GTK C; 2A6H A; 4AYB L; 4A3E C; 5IP7 K; 3GTK K; 1TWC C; 1YNJ A; 2PA8 L; 4A3E K; 4OIR A; 5FLM C; 2Y0S D; 2NVQ C; 1TWC K; 3GTG C; 4BY1 C; 3HKZ D; 2JA6 C; 5FLM K; 2NVQ K; 2A68 A; 1R9T C; 5M3F K; 4BY1 K; 3GTG K; 2JA6 K; 4Q5S A; 4A3J C; 3HOV C; 1R9T K; 3S2D C; 5TMC A; 4A3J K; 3S2D K; 4OIO A; 4NOI A; 2PMZ L; 5D4D A; 3PO3 C; 3WOD A; 4XSX A; 2JA7 C; 5IYB C; 3S17 C; 3PO3 K; 4QIW L; 1YNN A; 1ZYR A; 4GZY A; 2JA7 K; 3S17 K; 3HOY C; 4C3I C; 5IYB K; 5M5X K; 3HOY K; 3M4O C; 2E2J C; 4C3I K; 5TMF A; 2E2H C; 4BBS C; 2E2J K; 4XSZ A; 3GTQ C; 3I4N C; 2E2H K; 4BBS K; 3GTQ K; 3I4N K; 5FJ8 K; 1I6H C; 4KN4 A; 4Y52 C; 1I6H K; 2O5I A; 4A3G C; 4Y52 K; 3S1N C; 5C3E C; 2E2I C; 4AYB D; 2WB1 L; 4A3G K; 4A3I C; 4A3D C; 3S1N K; 5C3E K; 2E2I K; 2PA8 D; 4KMU A; 4A3I K; 4A3D K; 4YFN A; 3GTL C; 1SFO C; 2WAQ D; 1BDF A; 4YFK A; 2R93 C; 3GTL K; 1SFO K; 3HOV K; 2R93 K; 1I50 C; 1TWA C; 2NVT C; 1Y1W C; 3M3Y C; 3S16 C; 5IYD C; 1I50 K; 1TWA K; 2NVT K; 3H3V L; 1Y1W K; 5C44 C; 3M3Y K; 3S16 K; 5IYD K; 1IW7 A; 2PMZ D; 5C44 K; 3GTM C; 4A93 C; 1K83 C; 4LJZ A; 3GTM K; 4A93 K; 4QIW D; 4C2M C; 2NVX C; 4ZH4 A; 4A3B C; 2JA8 C; 2CW0 A; 5IP9 C; 4X6A C; 4C2M K; 3M4O K; 2NVX K; 4A3B K; 4G7Z A; 4A3L C; 2JA8 K; 4X6A K; 4KN7 A; 4A3L K; 1Y1V C; 2JA5 C; 3GTO C; 2PPB A; 3S1Q C; 3PO2 C; 1Y1V K; 3S1R C; 2JA5 K; 3GTO K; 3HOW C; 3S1Q K; 3PO2 K; 3DXJ A; 2VUM C; 4MQ9 A; 3HOZ C; 4BY7 C; 3S1R K; 3S1M C; 3FKI C; 3HOW K; 2B63 C; 4LK0 A; 2VUM K; 3HOZ K; 4BY7 K; 3S1M K; 4C3H C; 3FKI K; 2B63 K; 2WB1 D; 4C3H K; 1TWG C; 1HQM A; 1TWG K; 4Q4Z A; 3S2H C; 3K7A C; 2A69 A; 3I4M C; 4LK1 A; 3HOX C; 4OIN A; 4MEY A; 3K7A K; 3S2H K; 4A3M C; 4MEX A; 5C4J C; 3I4M K; 3HOX K; 4LLG A; 5M3M K; 3H3V D; 4A3K C; 5M5Y K; 4A3M K; 5C4J K; 4YFX A; 4A3K K; 3HOU C; 1K83 K; 2Y0S L; 2NVY C; 3HOU K; 2A6E A; 3HKZ L; 5IYC C; 3S15 C; 1I3Q C; 4Y7N C; 3RZD C; 2NVY K; 5IP9 K; 2R92 C; 5IYC K; 3S15 K; 4BBR C; 4XLP A; 1I3Q K; 4Y7N K; 2WAQ L; 3RZD K; 4BXX C; 2R92 K; 5C4X C; 4BBR K; 3S14 C; 4BXX K; 1TWH C; 5C4X K; 3S14 K; 2BE5 A; 3RZO C; 3GTP C; 3GTJ C; 1TWH K; 2YU9 C; 4OIP A; 4G7O A; 3RZO K; 3GTP K; 3GTJ K; 1TWF C; 2YU9 K; 3EQL A; #chains in the Genus database with same CATH topology 2R7Z C; 3FHZ A; 3N0B A; 4IO9 S; 4A3F C; 1INN A; 4AH6 A; 1R9T A; 1VJE A; 4XLN A; 1WCM K; 1TWH A; 1XPP A; 1XZP A; 1I6V A; 5DM7 S; 4JK1 A; 1XZP B; 3H0G K; 2O5J A; 4YG2 A; 4AYB L; 1TWC C; 1YNJ A; 2PA8 L; 4A3E K; 4OIR A; 3GTG C; 5IOT A; 2NVQ K; 1O28 A; 2P5M A; 4BY1 K; 2JA6 K; 3T00 A; 1FEU A; 4KB2 A; 3IPJ A; 3TTG A; 1WOO A; 2L5N A; 1RU0 A; 2PMZ L; 3GIR A; 3SZY A; 5IOR A; 2XCQ A; 4PAB A; 4XSX A; 2JA7 C; 5IYB C; 4QIW L; 1YNN A; 1ZYR A; 3S17 K; 3HOY C; 4U67 S; 1WIH A; 4BLB A; 3M4O C; 1SFO A; 3AD7 C; 4BBS C; 4KM8 A; 4XSZ A; 1HI9 A; 2E2J K; 1Y1W A; 3GTQ K; 4KN4 A; 1EI6 A; 3T01 A; 2GAG C; 2O5I A; 4A3G C; 3V4G A; 2GAH C; 2E2I K; 4KMU A; 3T02 A; 4A3I K; 2E2H A; 4YFN A; 3GSI A; 2R93 C; 1O29 A; 3HOV K; 1TWA C; 3S16 C; 1I50 K; 1WQG A; 5CHP A; 5C44 K; 1O25 A; 2NVX C; 4ZH4 A; 4A3B C; 2JA8 C; 4C2M K; 1ZXO A; 4G7Z A; 1EQR A; 1WOS A; 4GT9 A; 2JA5 C; 1O24 A; 3VA7 A; 3GTO K; 3HOW C; 3DXJ A; 3BP8 C; 4WJ3 M; 3S1M C; 1IS1 A; 3HOZ K; 1USO A; 1JOE A; 1O26 A; 4C3H K; 2R92 A; 1HQM A; 4KM9 A; 3K7A C; 4DDQ A; 3S2H K; 4LK1 A; 3LYW A; 5C4J C; 3HOX K; 2YU9 A; 2B63 A; 3H3V D; 3LAJ A; 4WJ4 A; 1TWG A; 1WSR A; 3HOU K; 2A6E A; 3FOE A; 4BBR C; 4XLP A; 3RZD K; 3GDZ A; 3H0G A; 3S14 C; 3OEP A; 1TWH C; 1B4A A; 3GEI A; 1IE0 A; 3AH5 A; 4OIP A; 1KQ4 A; 1XXA A; 1ZVU A; 4BKW A; 4RMF A; 3ADA C; 2P8T A; 4P9S A; 1SMY A; 2R7Z K; 3A8I A; 2JA6 A; 4A3F K; 4KMH A; 2PHC B; 4FZB A; 4QJV A; 1PJ5 A; 4QJV B; 4M1X A; 2KXY A; 4GTD A; 2KQ1 A; 5IP7 C; 1XXB A; 3G4C A; 4LOW A; 1TWC K; 3HKZ D; 4KMA A; 4PAA A; 1ISE A; 4GTE A; 5M3F K; 3GTG K; 4Q5S A; 4A3J C; 3GTK A; 4OIO A; 1WOR A; 3N0C A; 2E2I A; 2JA7 K; 5IYB K; 4C3I C; 3LAP A; 5M5X K; 2D6F C; 3HOY K; 5TJ3 A; 5TMF A; 2E2H C; 1I50 A; 4BBS K; 4KAW X; 5FJ8 K; 3PIP S; 4Y52 C; 1J6W A; 2JH3 A; 5C3E C; 4AYB D; 4A3G K; 4A3D C; 2PA8 D; 4IOC S; 1F7U A; 3GTL C; 2L3U A; 4GTF A; 3GTO A; 2R93 K; 2EBB A; 3M3Y C; 1O2F B; 5IYD C; 1TWA K; 3L4K A; 3S16 K; 3BUE A; 2PMZ D; 4IOA S; 1F9N A; 5DM6 S; 4ILD A; 1V5V A; 4QIW D; 2RGR A; 1YCL A; 3S0X A; 2NVX K; 4A3B K; 4A3L C; 3TFH A; 2JA8 K; 1VLO A; 1Y1V C; 3A8K A; 2PPB A; 2ZUF A; 4KAR A; 3QX3 A; 4WIL A; 3PO2 C; 2JA5 K; 4GTB A; 3GTM A; 4BY7 C; 3HOW K; 2B63 C; 3S1M K; 3PIO S; 1YX2 A; 1B4B A; 4KAS A; 2ZJQ S; 1BS2 A; 1TWG C; 1WQH A; 4Q4Z A; 3L4J A; 1L0W A; 1BJT A; 3I4M C; 1EK8 A; 3K7A K; 4G0U A; 2VUM A; 4MEX A; 3FKI A; 5M5Y K; 4LQY A; 5C4J K; 3AD8 C; 1K83 K; 1DCH A; 2Y0S L; 2ZJP S; 5IYC C; 3S15 C; 4Y7N C; 2KWA A; 5IP9 K; 1WSV A; 3DLL S; 2ZJR S; 4BXX C; 4BBR K; 2ZFZ A; 3S14 K; 2BE5 A; 3RZO C; 3GTP C; 1TWH K; 5HQH A; 1TWF C; 2NVY A; 3EQL A; 1I3Q A; 3FOF A; 3AQO A; 4KMD A; 2XCO A; 1AB4 A; 1JQW A; 3G4A A; 1UV7 A; 3GTJ A; 3GEE A; 3CQZ C; 4A3C C; 4C3J C; 4XCH A; 3AD9 C; 1XZQ A; 5M5W K; 1XZQ B; 3GTK C; 2A6H A; 2JA7 A; 2ZUE A; 5IP7 K; 1WCM A; 5FLM C; 2XCR B; 3ORE A; 2A68 A; 1R9T C; 4WF9 S; 2W7V A; 3HOV C; 3S2D C; 4A3J K; 1G51 A; 4NOI A; 5D4D A; 3PO3 C; 3WOD A; 1J6V A; 1PJ7 A; 3JST A; 4GZY A; 4WFB S; 4C3I K; 2V6T A; 3I4N C; 2E2H K; 1PJ6 A; 1I6H C; 1EFW A; 4Y52 K; 3A8J A; 3S1N C; 2WB1 L; 1F93 A; 4KB4 A; 2NVX A; 5C3E K; 4A3D K; 4WFA S; 3GTQ A; 1SFO C; 2WAQ D; 1O2B A; 4P5B A; 3GTL K; 3MML B; 2Y3P A; 2NVT C; 1Y1W C; 3M3Y K; 5IYD K; 1O27 A; 3GTM C; 4A93 C; 2KPU A; 4LJZ A; 3Q3Q A; 5EGE A; 5HL8 A; 2CW0 A; 4X6A C; 2V6S A; 3M4O K; 4C45 A; 4KN7 A; 4A3L K; 1IL2 A; 3S1Q C; 1Y1V K; 3S1R C; 4KC6 A; 1K83 A; 3PO2 K; 2VUM C; 4LR2 A; 3FKI C; 1J6X A; 4BY7 K; 2B63 K; 1X31 C; 1TWG K; 3GEH A; 4A3M C; 1F7V A; 3I4M K; 4LLG A; 5M3M K; 4A3K C; 4YFX A; 2NVY C; 2GSU A; 1I3Q C; 2R92 C; 5IYC K; 3S15 K; 4Y7N K; 5C4X C; 5JVO A; 4WCE S; 4BXX K; 4BLA A; 3TFI A; 3GTJ C; 2YU9 C; 3RZO K; 3GTP K; 1TWF K; 4G7H A; 4O2D A; 1WCM C; 1J98 A; 1IQ0 A; 4OIQ A; 3H0G C; 3CQZ K; 4GTA A; 4A3C K; 4C3J K; 2R7Z A; 1BGW A; 5JVG S; 4A3E C; 4P5A A; 3GTK K; 4GTL A; 5JFE A; 4WFN S; 2Y0S D; 2NVQ C; 4BY1 C; 2JA6 C; 5FLM K; 2FQO A; 4GFQ A; 5IOS A; 1R9T K; 1WQF A; 5TMC A; 3S2D K; 1ZBS A; 1TWC A; 3S17 C; 3GTG A; 3PO3 K; 1VGX A; 3AQP A; 1DCO A; 3GTL A; 2E2J C; 2CFA A; 2CFA B; 4GTC A; 3OPF A; 1VH2 A; 3GTQ C; 3N3Y A; 3I4N K; 1JVI A; 1I6H K; 2E2I C; 5JVH S; 1EH1 A; 4A3I C; 3S1N K; 4FM9 A; 1ZQ1 C; 5IOQ A; 2RH6 A; 1BDF A; 4YFK A; 1SFO K; 1Y1V A; 1I50 C; 3H3V L; 2NVT K; 1Y1W K; 5C44 C; 1IW7 A; 1GE9 A; 1K83 C; 3HXA A; 3GTM K; 4A93 K; 4C2M C; 2GSO A; 2R93 A; 5IP9 C; 1TWA A; 3NUH A; 1DCP A; 4X6A K; 1IBA A; 3GTO C; 1USM A; 3S1Q K; 1VRQ C; 3HOZ C; 3S1R K; 4MQ9 A; 2VUM K; 4LK0 A; 5HL7 S; 4C3H C; 3FKI K; 2GSN A; 2WB1 D; 3CAG A; 2FQT A; 4J3N A; 3CF5 S; 2JA5 A; 3SZZ A; 3S2H C; 5EGH A; 3BP3 A; 3LPX A; 2A69 A; 3HOX C; 4OIN A; 4MEY A; 4G0V A; 3GTP A; 4G0W A; 2V6U A; 5E68 A; 4A3M K; 1DD5 A; 1TWF A; 4A3K K; 3HOU C; 1XXC A; 1WOP A; 3TFJ A; 3HKZ L; 2NVY K; 3RZD C; 1O2A A; 1I3Q K; 2WAQ L; 4KAT A; 2R92 K; 3CQZ A; 1C0A A; 5C4X K; 3ERE D; 4KDD A; 5L46 A; 5CJ9 A; 4G7O A; 3GTJ K; 2YU9 K; #chains in the Genus database with same CATH homology 2R7Z C; 1TWF K; 4G7H A; 4A3F C; 2R7Z K; 1SMY A; 4A3F K; 1WCM C; 4XLN A; 1WCM K; 4OIQ A; 1XPP A; 3H0G C; 4QJV A; 1I6V A; 3CQZ C; 4JK1 A; 4A3C C; 4QJV B; 4C3J C; 3H0G K; 2O5J A; 3CQZ K; 4A3C K; 5M5W K; 4C3J K; 4YG2 A; 5IP7 C; 3GTK C; 2A6H A; 4AYB L; 4A3E C; 5IP7 K; 3GTK K; 1TWC C; 1YNJ A; 2PA8 L; 4A3E K; 4OIR A; 5FLM C; 2Y0S D; 2NVQ C; 1TWC K; 3GTG C; 4BY1 C; 3HKZ D; 2JA6 C; 5FLM K; 2NVQ K; 2A68 A; 1R9T C; 5M3F K; 4BY1 K; 3GTG K; 2JA6 K; 4Q5S A; 4A3J C; 3HOV C; 1R9T K; 3S2D C; 5TMC A; 4A3J K; 3S2D K; 4OIO A; 4NOI A; 2PMZ L; 5D4D A; 3PO3 C; 3WOD A; 4XSX A; 2JA7 C; 5IYB C; 3S17 C; 3PO3 K; 4QIW L; 1YNN A; 1ZYR A; 4GZY A; 2JA7 K; 3S17 K; 3HOY C; 4C3I C; 5IYB K; 5M5X K; 3HOY K; 3M4O C; 2E2J C; 4C3I K; 5TMF A; 2E2H C; 4BBS C; 2E2J K; 4XSZ A; 3GTQ C; 3I4N C; 2E2H K; 4BBS K; 3GTQ K; 3I4N K; 5FJ8 K; 1I6H C; 4KN4 A; 4Y52 C; 1I6H K; 2O5I A; 4A3G C; 4Y52 K; 3S1N C; 5C3E C; 2E2I C; 4AYB D; 2WB1 L; 4A3G K; 4A3I C; 4A3D C; 3S1N K; 5C3E K; 2E2I K; 2PA8 D; 4KMU A; 4A3I K; 4A3D K; 4YFN A; 3GTL C; 1SFO C; 2WAQ D; 1BDF A; 4YFK A; 2R93 C; 3GTL K; 1SFO K; 3HOV K; 2R93 K; 1I50 C; 1TWA C; 2NVT C; 1Y1W C; 3M3Y C; 3S16 C; 5IYD C; 1I50 K; 1TWA K; 2NVT K; 3H3V L; 1Y1W K; 5C44 C; 3M3Y K; 3S16 K; 5IYD K; 1IW7 A; 2PMZ D; 5C44 K; 3GTM C; 4A93 C; 1K83 C; 4LJZ A; 3GTM K; 4A93 K; 4QIW D; 4C2M C; 2NVX C; 4ZH4 A; 4A3B C; 2JA8 C; 2CW0 A; 5IP9 C; 4X6A C; 4C2M K; 3M4O K; 2NVX K; 4A3B K; 4G7Z A; 4A3L C; 2JA8 K; 4X6A K; 4KN7 A; 4A3L K; 1Y1V C; 2JA5 C; 3GTO C; 2PPB A; 3S1Q C; 3PO2 C; 1Y1V K; 3S1R C; 2JA5 K; 3GTO K; 3HOW C; 3S1Q K; 3PO2 K; 3DXJ A; 2VUM C; 4MQ9 A; 3HOZ C; 4BY7 C; 3S1R K; 3S1M C; 3FKI C; 3HOW K; 2B63 C; 4LK0 A; 2VUM K; 3HOZ K; 4BY7 K; 3S1M K; 4C3H C; 3FKI K; 2B63 K; 2WB1 D; 4C3H K; 1TWG C; 1HQM A; 1TWG K; 4Q4Z A; 3S2H C; 3K7A C; 2A69 A; 3I4M C; 4LK1 A; 3HOX C; 4OIN A; 4MEY A; 3K7A K; 3S2H K; 4A3M C; 4MEX A; 5C4J C; 3I4M K; 3HOX K; 4LLG A; 5M3M K; 3H3V D; 4A3K C; 5M5Y K; 4A3M K; 5C4J K; 4YFX A; 4A3K K; 3HOU C; 1K83 K; 2Y0S L; 2NVY C; 3HOU K; 2A6E A; 3HKZ L; 5IYC C; 3S15 C; 1I3Q C; 4Y7N C; 3RZD C; 2NVY K; 5IP9 K; 2R92 C; 5IYC K; 3S15 K; 4BBR C; 4XLP A; 1I3Q K; 4Y7N K; 2WAQ L; 3RZD K; 4BXX C; 2R92 K; 5C4X C; 4BBR K; 3S14 C; 4BXX K; 1TWH C; 5C4X K; 3S14 K; 2BE5 A; 3RZO C; 3GTP C; 3GTJ C; 1TWH K; 2YU9 C; 4OIP A; 4G7O A; 3RZO K; 3GTP K; 3GTJ K; 1TWF C; 2YU9 K; 3EQL A;
#similar chains in the Genus database (?% sequence similarity) ...loading similar chains, please wait... #similar chains, but unknotted ...loading similar chains, please wait... #similar chains in the pdb database (?% sequence similarity) ...loading similar chains, please wait...
