2NVYE

Rna polymerase ii form ii in 150 mm mn+2
Total Genus 66
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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
66
sequence length
215
structure length
215
Chain Sequence
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
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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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molecule tags Transcription
molecule keywords DNA-directed RNA polymerase II largest subunit
publication title Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
pubmed doi rcsb
total genus 66
structure length 215
sequence length 215
ec nomenclature
pdb deposition date 2006-11-13

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 2nvyE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 2nvyE02
3S2HE 1TWCE 2R92E 4X6AE 2PMZH 1EIKA 1DZFA 5M5WE 1Y1WE 3GTKE 3S1RE 2YU9E 3HOYE 3S2DE 3HOZE 2B63E 3HOVE 1SFOE 4Y7NE 3PO3E 2JA5E 4A93E 1WCME 4A3FE 3RZOE 3S16E 3GTOE 1TWAE 2WB1H 5IYCE 4BBRE 3HOWE 3S1NE 2NVQE 2NVXE 2NVYE 4A3EE 3GTPE 1Y1VE 2JA8E 3I4NE 4C3HE 2JA6E 1K83E 3M3YE 5M3ME 5C44E 4A3CE 3M4OE 5C3EE 5M5YE 1I50E 3S14E 1I6HE 5C4JE 2WAQH 4C3IE 5IYBE 3FKIE 2JA7E 2E2HE 1R9TE 4BY7E 3RZDE 4A3KE 4A3IE 4A3BE 3GTQE 4A3GE 3HKZH 2R7ZE 4C2ME 4AYBH 2E2JE 4A3DE 4BY1E 5FJ8E 5M3FE 4A3ME 3GTJE 3GTLE 3HOXE 2NVTE 3CQZE 2R93E 4QIWH 5IP9E 2E2IE 3S15E 4BBSE 5IP7E 3GTME 1TWHE 3K7AE 3HOUE 2Y0SH 3S17E 4Y52E 1I3QE 1TWGE 3H0GE 3GTGE 4BXXE 5C4XE 3PO2E 2VUME 4A3LE 3S1ME 5FLME 1TWFE 4A3JE 4C3JE 3H3VF 3I4ME 5M5XE 5IYDE 3S1QE
chains in the Genus database with same CATH superfamily
4Q4ZE 1I50F 1I6HF 3S14F 3S2HE 5C4JF 3HOXF 4OINE 2NVTF 1TWCE 1QKLA 2R92E 4X6AE 2PMZH 4KN4E 1DZFA 1YNJK 4C3IF 5M5WE 3S15F 1EIKA 1Y1WE 5IP7F 3GTKE 3GTMF 3K7AF 3S1RE 2YU9E 3HOYE 3S2DE 3HOZE 3HOUF 5TMFE 2B63E 3FKIF 3S17F 1I3QF 4ZH4E 3HOVE 1ZYRE 1SFOE 4Y7NE 1IW7E 3PO3E 3H0GF 4XLPE 1R9TF 4BY7F 4OIRE 4A3IF 5E18E 2JA5E 3PO2F 4G7HE 4A3BF 4A93E 2R7ZF 1WCME 1HQME 2O5JE 4C2MF 4A3LF 4A3FE 3RZOE 2PMZK 2E2JF 4GZYE 4JK1E 1TWFF 4A3DF 5IPLE 3S16E 4Q5SE 3GTOE 1TWAE 2WB1H 5IYCE 4C3JF 4A3MF 3GTLF 3S1QF 4BBRE 2A6HE 2A68E 3HOWE 3CQZF 2O5IE 3S1NE 2NVQE 2NVXE 2NVYE 2R93F 4A3EE 3GTPE 5IP9F 2E2IF 4LK1E 1TWCF 1Y1VE 4BBSF 2JA8E 1TWHF 3EQLE 3I4NE 4C3HE 2JA6E 5M5WF 4LK0E 4XLNE 1K83E 3M3YE 1Y1WF 2WAQK 5M3ME 5C44E 2YU9F 4Y52F 3S2DF 2WB1I 3HOYF 1TWGF 4MEYE 2B63F 4A3CE 3M4OE 3GTGF 4BXXF 1SFOF 5C4XF 5C3EE 3PO3F 4LJZE 2BE5E 2VUMF 2JA5F 5M5YE 4OIQE 3S1MF 4A93F 1I50E 3S14E 1I6HE 1WCMF 5C4JE 5FLMF 5D4CE 4A3FF 4A3JF 2WAQH 3HKZK 4YG2E 3I4MF 4C3IE 3S16F 5M5XF 5IYCF 5IYDF 5D4DE 2KRXA 2A6EE 3DXJE 5D4EE 5IYBE 3FKIE 2JA7E 2E2HE 3S2HF 3HOWF 3S1NF 1R9TE 4KN7E 5BYHE 4A3EF 2R92F 3GTPF 4X6AF 4BY7E 3RZDE 4XSXE 4A3KE 4A3IE 2JA8F 3GTKF 4A3BE 3GTQE 4A3GE 3HKZH 2R7ZE 3S1RF 4OIOE 3HOZF 1K83F 4C2ME 4AYBH 2E2JE 5M3MF 5C44F 4G7OE 4A3DE 3HOVF 4Y7NF 4BY1E 5FJ8E 2CW0E 2Y0SI 5M3FE 5E17E 4A3ME 3GTJE 3GTLE 5C3EF 1SMYE 3H3VG 3HOXE 2NVTE 5M5YF 3CQZE 4OIPE 3RZOF 1YNNK 2R93E 4MQ9E 4QIWH 5IP9E 2E2IE 3S15E 4BBSE 5IP7E 1TWAF 4AYBK 3GTME 1TWHE 3K7AE 3HOUE 3GTOF 2Y0SH 4BBRF 4YFXE 2A69E 3S17E 4Y52E 1I3QE 1TWGE 5IYBF 4MEXE 3H0GE 2E2HF 2NVXF 2NVYF 3GTGE 2JA7F 2NVQF 4BXXE 5C4XE 4YFKE 3PO2E 1Y1VF 3RZDF 2PPBE 2VUME 5TMCE 4C3HF 4A3KF 2JA6F 3I4NF 4QIWK 4A3LE 3M3YF 3GTQF 4A3GF 3S1ME 5FLME 4XSZE 4G7ZE 4LLGE 1TWFE 4YFNE 4A3JE 4A3CF 3M4OF 4C3JE 3H3VF 3I4ME 4BY1F 5M5XE 3WODE 4KMUE 5FJ8F 5M3FF 5IYDE 1I6VE 3GTJF 3S1QE
chains in the Genus database with same CATH topology
3S2HE 1TWCE 2R92E 4X6AE 2PMZH 1EIKA 1DZFA 5M5WE 1Y1WE 3GTKE 3S1RE 2YU9E 3HOYE 3S2DE 3HOZE 2B63E 3HOVE 1SFOE 4Y7NE 3PO3E 2JA5E 4A93E 1WCME 4A3FE 3RZOE 3S16E 3GTOE 1TWAE 2WB1H 5IYCE 4BBRE 3HOWE 3S1NE 2NVQE 2NVXE 2NVYE 4A3EE 3GTPE 1Y1VE 2JA8E 3I4NE 4C3HE 2JA6E 1K83E 3M3YE 5M3ME 5C44E 4A3CE 3M4OE 5C3EE 5M5YE 1I50E 3S14E 1I6HE 5C4JE 2WAQH 4C3IE 5IYBE 3FKIE 2JA7E 2E2HE 1R9TE 4BY7E 3RZDE 4A3KE 4A3IE 4A3BE 3GTQE 4A3GE 3HKZH 2R7ZE 4C2ME 4AYBH 2E2JE 4A3DE 4BY1E 5FJ8E 5M3FE 4A3ME 3GTJE 3GTLE 3HOXE 2NVTE 3CQZE 2R93E 4QIWH 5IP9E 2E2IE 3S15E 4BBSE 5IP7E 3GTME 1TWHE 3K7AE 3HOUE 2Y0SH 3S17E 4Y52E 1I3QE 1TWGE 3H0GE 3GTGE 4BXXE 5C4XE 3PO2E 2VUME 4A3LE 3S1ME 5FLME 1TWFE 4A3JE 4C3JE 3H3VF 3I4ME 5M5XE 5IYDE 3S1QE
chains in the Genus database with same CATH homology


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