1TWCE

Rna polymerase ii complexed with gtp
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
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: nucleotide selection by rotation in the RNA polymerase II active center.
pubmed doi rcsb
total genus 63
structure length 215
sequence length 215
ec nomenclature
pdb deposition date 2004-06-30

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 1twcE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 1twcE02
4C3IE 2R93E 1I3QE 3GTPE 2WB1H 1TWCE 5IYDE 1DZFA 2NVQE 3S1QE 5M5XE 4BXXE 3S14E 3H3VF 4A3IE 1R9TE 5M5WE 4BY7E 4C3HE 4X6AE 5C4XE 3S17E 1I50E 3S1ME 1K83E 3PO2E 4A3LE 5FJ8E 1TWHE 5M5YE 4A3KE 1WCME 5FLME 4A3ME 2E2IE 2JA5E 2NVTE 3S16E 2R7ZE 3S15E 3I4ME 3M4OE 1TWFE 3RZOE 4A3CE 2Y0SH 3I4NE 1TWGE 5M3ME 3PO3E 3HOZE 2JA7E 2NVYE 2NVXE 3CQZE 2PMZH 1I6HE 5C3EE 3GTQE 3FKIE 3S2HE 3GTLE 4A3BE 5IYBE 4BY1E 3S1NE 3HOUE 4A3GE 3K7AE 3HOXE 5M3FE 1TWAE 4A3EE 1EIKA 4Y52E 2E2JE 4C2ME 2YU9E 3HOVE 5C4JE 5IYCE 3HOYE 4AYBH 1Y1WE 2JA6E 5IP7E 3S2DE 3HOWE 2R92E 4A3DE 3H0GE 4A3FE 5IP9E 2WAQH 4BBSE 2JA8E 2E2HE 1SFOE 3GTME 3GTJE 3S1RE 1Y1VE 4BBRE 4Y7NE 5C44E 4A3JE 3GTGE 4C3JE 3M3YE 3GTKE 4A93E 3GTOE 2B63E 3HKZH 2VUME 4QIWH 3RZDE
chains in the Genus database with same CATH superfamily
4C3IF 2R92F 2R93F 4C3IE 1I3QF 2R93E 4XSZE 1I3QE 3GTPE 2WB1H 4G7HE 3GTPF 4BBSF 1TWCF 2A69E 1TWCE 5IYDE 1DZFA 5TMCE 2PPBE 2NVQF 4MEXE 2NVQE 4XLNE 3S1QF 4BXXF 3S1QE 5E17E 5M5XE 4BXXE 3GTJF 5D4CE 3S14F 3S14E 4AYBK 3H3VF 3HKZK 4A3IE 2O5JE 5D4EE 1R9TF 4QIWK 5M5WF 1R9TE 4MEYE 5M5WE 2A6HE 4BY7F 1ZYRE 4BY7E 4C3HE 4C3HF 4X6AF 2WB1I 4X6AE 2A68E 2WAQK 4KN4E 4YG2E 5C4XE 5C44F 3S17F 4Q5SE 3S17E 4A3JF 1I50E 3WODE 3S1MF 4C3JF 3S1ME 3GTKF 3EQLE 5BYHE 1K83E 3GTOF 3PO2F 4A3LF 3S1NF 3PO2E 4A3LE 5FJ8F 5FJ8E 2A6EE 1TWHF 5M5YF 4JK1E 1WCMF 1TWHE 5M5YE 4A3KE 1WCME 5FLME 4A3ME 2E2IE 2JA5E 5FLMF 2E2IF 2JA5F 2NVTE 2NVTF 3S16F 3S16E 2R7ZF 1IW7E 5IYDF 4OIRE 2R7ZE 3S15F 3I4MF 4KN7E 3S15E 3I4ME 4LLGE 4GZYE 5M5XF 1TWFF 4ZH4E 3M4OF 3M4OE 1TWFE 3RZOE 4XLPE 3RZOF 4A3CF 4A3CE 2Y0SH 4A3IF 4YFXE 1TWGF 3I4NE 5M3MF 3I4NF 1TWGE 5M3ME 3HOZF 3PO3F 3PO3E 3HOZE 2JA7F 2NVYF 2NVXF 2JA7E 3CQZF 2NVYE 2NVXE 3CQZE 2PMZH 1I50F 4LJZE 1I6HF 5E18E 5C3EF 1I6HE 3GTQF 5C3EE 1K83F 3GTQE 1SMYE 3S2HF 3FKIE 3S2HE 2Y0SI 1I6VE 3GTLE 4A3BF 4A3BE 4BY1F 5IYBF 2CW0E 5IYBE 4BY1E 4OINE 4LK1E 3S1NE 3HOUE 4A3GE 3K7AF 3K7AE 3HOXE 5M3FF 4A3MF 5M3FE 1YNJK 1TWAF 1TWAE 4Q4ZE 4A3EF 4A3EE 4MQ9E 4YFNE 2KRXA 1YNNK 4Y52F 2O5IE 4Y52E 1EIKA 2E2JF 4C2MF 2E2JE 4C2ME 2YU9F 3HOVF 2YU9E 5C4JF 3HOVE 5C4JE 5IYCF 2BE5E 3HOYF 5IYCE 5D4DE 4A3GF 3HOYE 4AYBH 1Y1WF 2JA6F 5IP7F 1Y1WE 2JA6E 3S2DF 5IP7E 3S2DE 3FKIF 3HOWE 4A3DF 3H0GF 2R92E 4A3DE 5IP9F 3H0GE 4A3FE 5IP9E 2WAQH 4KMUE 4A3FF 4A3KF 4BBSE 2JA8E 2JA8F 2E2HF 3HOUF 4XSXE 2E2HE 3HOXF 1SFOF 1SFOE 1QKLA 3GTMF 2PMZK 3GTME 3S1RF 4OIQE 3GTJE 3H3VG 3S1RE 4OIOE 1Y1VF 1Y1VE 3DXJE 5TMFE 4BBRF 4G7OE 4Y7NF 4G7ZE 4BBRE 4Y7NE 4OIPE 5C44E 1HQME 4A3JE 4LK0E 5IPLE 3GTGF 3GTGE 3M3YF 4C3JE 3GTLF 3M3YE 3GTKE 4A93F 4A93E 3GTOE 2B63F 5C4XF 4YFKE 2B63E 3HKZH 2VUMF 3RZDF 2VUME 4QIWH 3RZDE 3HOWF
chains in the Genus database with same CATH topology
4C3IE 2R93E 1I3QE 3GTPE 2WB1H 1TWCE 5IYDE 1DZFA 2NVQE 3S1QE 5M5XE 4BXXE 3S14E 3H3VF 4A3IE 1R9TE 5M5WE 4BY7E 4C3HE 4X6AE 5C4XE 3S17E 1I50E 3S1ME 1K83E 3PO2E 4A3LE 5FJ8E 1TWHE 5M5YE 4A3KE 1WCME 5FLME 4A3ME 2E2IE 2JA5E 2NVTE 3S16E 2R7ZE 3S15E 3I4ME 3M4OE 1TWFE 3RZOE 4A3CE 2Y0SH 3I4NE 1TWGE 5M3ME 3PO3E 3HOZE 2JA7E 2NVYE 2NVXE 3CQZE 2PMZH 1I6HE 5C3EE 3GTQE 3FKIE 3S2HE 3GTLE 4A3BE 5IYBE 4BY1E 3S1NE 3HOUE 4A3GE 3K7AE 3HOXE 5M3FE 1TWAE 4A3EE 1EIKA 4Y52E 2E2JE 4C2ME 2YU9E 3HOVE 5C4JE 5IYCE 3HOYE 4AYBH 1Y1WE 2JA6E 5IP7E 3S2DE 3HOWE 2R92E 4A3DE 3H0GE 4A3FE 5IP9E 2WAQH 4BBSE 2JA8E 2E2HE 1SFOE 3GTME 3GTJE 3S1RE 1Y1VE 4BBRE 4Y7NE 5C44E 4A3JE 3GTGE 4C3JE 3M3YE 3GTKE 4A93E 3GTOE 2B63E 3HKZH 2VUME 4QIWH 3RZDE
chains in the Genus database with same CATH homology


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