3PO2E

Arrested rna polymerase ii elongation complex
Total Genus 63
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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
63
sequence length
214
structure length
214
Chain Sequence
DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
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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.

Chord Diagram
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publication title Structural basis of RNA polymerase II backtracking, arrest and reactivation.
pubmed doi rcsb
molecule tags Transferase/dna/rna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 63
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2010-11-21

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
E PF01191 RNA_pol_Rpb5_C RNA polymerase Rpb5, C-terminal domain
E PF03871 RNA_pol_Rpb5_N RNA polymerase Rpb5, N-terminal domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1340.10 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 RNA polymerase, Rpb5, N-terminal domain 3po2E01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 3po2E02
1WCME 5C3EE 5C4JE 3GTJE 3S1NE 1Y1WE 5IYCE 1Y1VE 2R92E 2JA5E 3RZOE 2JA7E 3HOWE 2E2IE 4BY7E 1EIKA 4Y7NE 2NVQE 2Y0SH 4AYBH 4A3EE 2JA8E 3S1RE 3HOYE 4C3HE 3S14E 3M3YE 4C3IE 2NVYE 1I50E 3I4ME 3RZDE 4A3FE 3GTGE 4QIWH 4A93E 1TWGE 3S2DE 2R7ZE 3H0GE 2E2JE 5IYDE 2JA6E 2WB1H 2NVTE 1TWCE 2B63E 3GTPE 4A3LE 3S16E 4C2ME 4A3CE 5M5XE 3HOUE 4A3IE 5C4XE 3HOXE 4X6AE 4A3BE 3PO3E 3PO2E 3HKZH 1I6HE 3GTQE 2R93E 2PMZH 5M3FE 3GTME 5FJ8E 3CQZE 2YU9E 3S17E 3I4NE 3HOZE 4A3GE 4A3KE 5IP9E 5IP7E 3S15E 4A3DE 1TWHE 4Y52E 3K7AE 1R9TE 3S1ME 4C3JE 2NVXE 3GTLE 4BY1E 1TWFE 1SFOE 3FKIE 1I3QE 2VUME 4BXXE 2E2HE 4BBSE 1K83E 4A3ME 1TWAE 5M5YE 1DZFA 3H3VF 3S2HE 3HOVE 4BBRE 5FLME 5C44E 3M4OE 3S1QE 5IYBE 2WAQH 5M3ME 5M5WE 3GTOE 4A3JE 3GTKE
chains in the Genus database with same CATH superfamily
1WCME 2CW0E 5C3EE 4OIQE 4BY1F 2WB1I 5TMFE 5C4JE 3GTJE 3S1NF 4OINE 3S1NE 1Y1WE 5C4JF 5IYCE 1TWGF 1Y1VE 1YNJK 2R92E 2R92F 3PO2F 3DXJE 2JA5E 3RZOE 2O5IE 2JA7E 5IP9F 5IP7F 3HOWE 2E2IE 2E2IF 4BY7E 3HOVF 1EIKA 4BY7F 5IPLE 5BYHE 2R93F 4Y7NE 2NVQE 3HKZK 2Y0SH 4Y7NF 5C3EF 4AYBH 4C2MF 4YFXE 4A3EE 1I6VE 5M3FF 2JA8E 3S1RE 4JK1E 4ZH4E 2JA8F 4A3EF 2NVQF 2VUMF 3GTKF 1Y1VF 4BBSF 3HOYE 4YFNE 4A3BF 4X6AF 4QIWK 1K83F 4AYBK 4C3HE 3S14E 4OIRE 3M3YE 4KN4E 4C3IE 3S17F 4A3LF 2NVYE 5E17E 1WCMF 4A3FF 1TWAF 2WAQK 1I50E 3I4ME 3RZDF 3RZDE 1I50F 3GTGF 4A3FE 3GTGE 3I4MF 4QIWH 4A93E 4XLNE 5D4DE 1IW7E 5C44F 1TWGE 5IYCF 3S2DE 2A68E 2R7ZE 4YFKE 3H0GE 4A3GF 2E2JE 5IYDF 5IYDE 2JA6E 4A3JF 2PPBE 4G7OE 2WB1H 2NVTE 2O5JE 4Y52F 1TWCE 2B63E 3GTPE 4A3LE 4C3IF 3GTPF 1TWCF 3WODE 2B63F 5M5XF 3HOUF 3S16E 1R9TF 5D4EE 3I4NF 4KMUE 4C2ME 4A3CE 5M5XE 3HOUE 4A3IE 5C4XE 2A6HE 1I3QF 4BXXF 3HOXE 3FKIF 4X6AE 4A3BE 3PO3E 3PO2E 4Q5SE 3HKZH 1I6HE 4XLPE 3M3YF 2JA7F 1TWHF 3GTQE 5M5YF 4A3DF 1SMYE 1HQME 4YG2E 1QKLA 4OIOE 4XSZE 4A93F 2R93E 4OIPE 4C3JF 4MEXE 3GTLF 2R7ZF 2PMZH 3S2DF 5M3FE 3GTME 4KN7E 1SFOF 4LJZE 5FJ8E 5M3MF 3CQZE 5M5WF 3CQZF 5FJ8F 2Y0SI 2YU9E 4GZYE 4Q4ZE 2PMZK 2YU9F 3S17E 3I4NE 4LK1E 3GTJF 4A3IF 2A6EE 1Y1WF 3HOZE 4XSXE 3RZOF 3HOZF 2JA5F 2E2JF 3HOWF 4A3GE 4A3KE 5IP9E 5IP7E 3S15E 2BE5E 3H0GF 4A3DE 4MQ9E 4G7ZE 1TWHE 4G7HE 3GTOF 2A69E 4Y52E 2NVTF 3K7AF 5TMCE 3K7AE 1R9TE 3S16F 3S1ME 4C3JE 2NVXE 3GTLE 1TWFF 1YNNK 4BY1E 1TWFE 4LLGE 1SFOE 4MEYE 5IYBF 2NVXF 3GTMF 4A3CF 5C4XF 1ZYRE 3FKIE 3HOXF 3H3VG 1I3QE 2VUME 4BXXE 2E2HE 4BBSE 1I6HF 4C3HF 3PO3F 1K83E 4A3ME 4A3MF 1TWAE 5M5YE 1DZFA 3GTQF 2NVYF 3H3VF 4LK0E 3S2HF 3S2HE 4BBRF 3HOVE 5FLMF 3M4OF 5D4CE 4BBRE 5FLME 5C44E 3M4OE 3S1QE 5IYBE 3S1QF 5E18E 2WAQH 3S1RF 5M3ME 5M5WE 3GTOE 4A3KF 3S15F 3HOYF 4A3JE 2JA6F 3GTKE 2KRXA 2E2HF 3S1MF 3S14F 3EQLE
chains in the Genus database with same CATH topology
1WCME 5C3EE 5C4JE 3GTJE 3S1NE 1Y1WE 5IYCE 1Y1VE 2R92E 2JA5E 3RZOE 2JA7E 3HOWE 2E2IE 4BY7E 1EIKA 4Y7NE 2NVQE 2Y0SH 4AYBH 4A3EE 2JA8E 3S1RE 3HOYE 4C3HE 3S14E 3M3YE 4C3IE 2NVYE 1I50E 3I4ME 3RZDE 4A3FE 3GTGE 4QIWH 4A93E 1TWGE 3S2DE 2R7ZE 3H0GE 2E2JE 5IYDE 2JA6E 2WB1H 2NVTE 1TWCE 2B63E 3GTPE 4A3LE 3S16E 4C2ME 4A3CE 5M5XE 3HOUE 4A3IE 5C4XE 3HOXE 4X6AE 4A3BE 3PO3E 3PO2E 3HKZH 1I6HE 3GTQE 2R93E 2PMZH 5M3FE 3GTME 5FJ8E 3CQZE 2YU9E 3S17E 3I4NE 3HOZE 4A3GE 4A3KE 5IP9E 5IP7E 3S15E 4A3DE 1TWHE 4Y52E 3K7AE 1R9TE 3S1ME 4C3JE 2NVXE 3GTLE 4BY1E 1TWFE 1SFOE 3FKIE 1I3QE 2VUME 4BXXE 2E2HE 4BBSE 1K83E 4A3ME 1TWAE 5M5YE 1DZFA 3H3VF 3S2HE 3HOVE 4BBRE 5FLME 5C44E 3M4OE 3S1QE 5IYBE 2WAQH 5M3ME 5M5WE 3GTOE 4A3JE 3GTKE
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1WCM E;  5C3E E;  5C4J E;  3GTJ E;  3S1N E;  1Y1W E;  5IYC E;  1Y1V E;  2R92 E;  2JA5 E;  3RZO E;  2JA7 E;  3HOW E;  2E2I E;  4BY7 E;  1EIK A;  4Y7N E;  2NVQ E;  2Y0S H;  4AYB H;  4A3E E;  2JA8 E;  3S1R E;  3HOY E;  4C3H E;  3S14 E;  3M3Y E;  4C3I E;  2NVY E;  1I50 E;  3I4M E;  3RZD E;  4A3F E;  3GTG E;  4QIW H;  4A93 E;  1TWG E;  3S2D E;  2R7Z E;  3H0G E;  2E2J E;  5IYD E;  2JA6 E;  2WB1 H;  2NVT E;  1TWC E;  2B63 E;  3GTP E;  4A3L E;  3S16 E;  4C2M E;  4A3C E;  5M5X E;  3HOU E;  4A3I E;  5C4X E;  3HOX E;  4X6A E;  4A3B E;  3PO3 E;  3PO2 E;  3HKZ H;  1I6H E;  3GTQ E;  2R93 E;  2PMZ H;  5M3F E;  3GTM E;  5FJ8 E;  3CQZ E;  2YU9 E;  3S17 E;  3I4N E;  3HOZ E;  4A3G E;  4A3K E;  5IP9 E;  5IP7 E;  3S15 E;  4A3D E;  1TWH E;  4Y52 E;  3K7A E;  1R9T E;  3S1M E;  4C3J E;  2NVX E;  3GTL E;  4BY1 E;  1TWF E;  1SFO E;  3FKI E;  1I3Q E;  2VUM E;  4BXX E;  2E2H E;  4BBS E;  1K83 E;  4A3M E;  1TWA E;  5M5Y E;  1DZF A;  3H3V F;  3S2H E;  3HOV E;  4BBR E;  5FLM E;  5C44 E;  3M4O E;  3S1Q E;  5IYB E;  2WAQ H;  5M3M E;  5M5W E;  3GTO E;  4A3J E;  3GTK E; 
#chains in the Genus database with same CATH topology
 1WCM E;  2CW0 E;  5C3E E;  4OIQ E;  4BY1 F;  2WB1 I;  5TMF E;  5C4J E;  3GTJ E;  3S1N F;  4OIN E;  3S1N E;  1Y1W E;  5C4J F;  5IYC E;  1TWG F;  1Y1V E;  1YNJ K;  2R92 E;  2R92 F;  3PO2 F;  3DXJ E;  2JA5 E;  3RZO E;  2O5I E;  2JA7 E;  5IP9 F;  5IP7 F;  3HOW E;  2E2I E;  2E2I F;  4BY7 E;  3HOV F;  1EIK A;  4BY7 F;  5IPL E;  5BYH E;  2R93 F;  4Y7N E;  2NVQ E;  3HKZ K;  2Y0S H;  4Y7N F;  5C3E F;  4AYB H;  4C2M F;  4YFX E;  4A3E E;  1I6V E;  5M3F F;  2JA8 E;  3S1R E;  4JK1 E;  4ZH4 E;  2JA8 F;  4A3E F;  2NVQ F;  2VUM F;  3GTK F;  1Y1V F;  4BBS F;  3HOY E;  4YFN E;  4A3B F;  4X6A F;  4QIW K;  1K83 F;  4AYB K;  4C3H E;  3S14 E;  4OIR E;  3M3Y E;  4KN4 E;  4C3I E;  3S17 F;  4A3L F;  2NVY E;  5E17 E;  1WCM F;  4A3F F;  1TWA F;  2WAQ K;  1I50 E;  3I4M E;  3RZD F;  3RZD E;  1I50 F;  3GTG F;  4A3F E;  3GTG E;  3I4M F;  4QIW H;  4A93 E;  4XLN E;  5D4D E;  1IW7 E;  5C44 F;  1TWG E;  5IYC F;  3S2D E;  2A68 E;  2R7Z E;  4YFK E;  3H0G E;  4A3G F;  2E2J E;  5IYD F;  5IYD E;  2JA6 E;  4A3J F;  2PPB E;  4G7O E;  2WB1 H;  2NVT E;  2O5J E;  4Y52 F;  1TWC E;  2B63 E;  3GTP E;  4A3L E;  4C3I F;  3GTP F;  1TWC F;  3WOD E;  2B63 F;  5M5X F;  3HOU F;  3S16 E;  1R9T F;  5D4E E;  3I4N F;  4KMU E;  4C2M E;  4A3C E;  5M5X E;  3HOU E;  4A3I E;  5C4X E;  2A6H E;  1I3Q F;  4BXX F;  3HOX E;  3FKI F;  4X6A E;  4A3B E;  3PO3 E;  3PO2 E;  4Q5S E;  3HKZ H;  1I6H E;  4XLP E;  3M3Y F;  2JA7 F;  1TWH F;  3GTQ E;  5M5Y F;  4A3D F;  1SMY E;  1HQM E;  4YG2 E;  1QKL A;  4OIO E;  4XSZ E;  4A93 F;  2R93 E;  4OIP E;  4C3J F;  4MEX E;  3GTL F;  2R7Z F;  2PMZ H;  3S2D F;  5M3F E;  3GTM E;  4KN7 E;  1SFO F;  4LJZ E;  5FJ8 E;  5M3M F;  3CQZ E;  5M5W F;  3CQZ F;  5FJ8 F;  2Y0S I;  2YU9 E;  4GZY E;  4Q4Z E;  2PMZ K;  2YU9 F;  3S17 E;  3I4N E;  4LK1 E;  3GTJ F;  4A3I F;  2A6E E;  1Y1W F;  3HOZ E;  4XSX E;  3RZO F;  3HOZ F;  2JA5 F;  2E2J F;  3HOW F;  4A3G E;  4A3K E;  5IP9 E;  5IP7 E;  3S15 E;  2BE5 E;  3H0G F;  4A3D E;  4MQ9 E;  4G7Z E;  1TWH E;  4G7H E;  3GTO F;  2A69 E;  4Y52 E;  2NVT F;  3K7A F;  5TMC E;  3K7A E;  1R9T E;  3S16 F;  3S1M E;  4C3J E;  2NVX E;  3GTL E;  1TWF F;  1YNN K;  4BY1 E;  1TWF E;  4LLG E;  1SFO E;  4MEY E;  5IYB F;  2NVX F;  3GTM F;  4A3C F;  5C4X F;  1ZYR E;  3FKI E;  3HOX F;  3H3V G;  1I3Q E;  2VUM E;  4BXX E;  2E2H E;  4BBS E;  1I6H F;  4C3H F;  3PO3 F;  1K83 E;  4A3M E;  4A3M F;  1TWA E;  5M5Y E;  1DZF A;  3GTQ F;  2NVY F;  3H3V F;  4LK0 E;  3S2H F;  3S2H E;  4BBR F;  3HOV E;  5FLM F;  3M4O F;  5D4C E;  4BBR E;  5FLM E;  5C44 E;  3M4O E;  3S1Q E;  5IYB E;  3S1Q F;  5E18 E;  2WAQ H;  3S1R F;  5M3M E;  5M5W E;  3GTO E;  4A3K F;  3S15 F;  3HOY F;  4A3J E;  2JA6 F;  3GTK E;  2KRX A;  2E2H F;  3S1M F;  3S14 F;  3EQL E; 
#chains in the Genus database with same CATH homology
 1WCM E;  5C3E E;  5C4J E;  3GTJ E;  3S1N E;  1Y1W E;  5IYC E;  1Y1V E;  2R92 E;  2JA5 E;  3RZO E;  2JA7 E;  3HOW E;  2E2I E;  4BY7 E;  1EIK A;  4Y7N E;  2NVQ E;  2Y0S H;  4AYB H;  4A3E E;  2JA8 E;  3S1R E;  3HOY E;  4C3H E;  3S14 E;  3M3Y E;  4C3I E;  2NVY E;  1I50 E;  3I4M E;  3RZD E;  4A3F E;  3GTG E;  4QIW H;  4A93 E;  1TWG E;  3S2D E;  2R7Z E;  3H0G E;  2E2J E;  5IYD E;  2JA6 E;  2WB1 H;  2NVT E;  1TWC E;  2B63 E;  3GTP E;  4A3L E;  3S16 E;  4C2M E;  4A3C E;  5M5X E;  3HOU E;  4A3I E;  5C4X E;  3HOX E;  4X6A E;  4A3B E;  3PO3 E;  3PO2 E;  3HKZ H;  1I6H E;  3GTQ E;  2R93 E;  2PMZ H;  5M3F E;  3GTM E;  5FJ8 E;  3CQZ E;  2YU9 E;  3S17 E;  3I4N E;  3HOZ E;  4A3G E;  4A3K E;  5IP9 E;  5IP7 E;  3S15 E;  4A3D E;  1TWH E;  4Y52 E;  3K7A E;  1R9T E;  3S1M E;  4C3J E;  2NVX E;  3GTL E;  4BY1 E;  1TWF E;  1SFO E;  3FKI E;  1I3Q E;  2VUM E;  4BXX E;  2E2H E;  4BBS E;  1K83 E;  4A3M E;  1TWA E;  5M5Y E;  1DZF A;  3H3V F;  3S2H E;  3HOV E;  4BBR E;  5FLM E;  5C44 E;  3M4O E;  3S1Q E;  5IYB E;  2WAQ H;  5M3M E;  5M5W E;  3GTO E;  4A3J E;  3GTK E; 
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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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#similar chains in the pdb database (?% sequence similarity)
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