1TWHE

Rna polymerase ii complexed with 2'datp
Total Genus 67
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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
67
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
publication title Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II largest subunit
total genus 67
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 1twhE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 1twhE02
3S15E 4A3GE 1K83E 3S1ME 2VUME 3GTKE 2WB1H 2NVYE 3HOUE 5C4JE 3HOWE 3HOZE 4Y52E 3FKIE 1I50E 1TWCE 5M3ME 3S16E 3S1RE 4AYBH 5FJ8E 2JA7E 4A3BE 3S1NE 3HKZH 4A3LE 3RZOE 3S17E 3H3VF 3I4NE 4X6AE 2E2JE 2JA5E 2NVQE 1TWAE 4A3JE 1WCME 5C3EE 4C3HE 3S2HE 2E2HE 5IP7E 4A3IE 1TWHE 4BBRE 2R93E 3RZDE 3HOVE 5IYBE 4BY1E 3GTQE 4BXXE 4C3JE 5M5XE 4Y7NE 1I6HE 2R92E 3GTGE 5M5WE 2NVXE 4C3IE 2E2IE 3GTOE 2JA6E 4A3FE 4A3KE 3GTME 3S14E 2WAQH 3S2DE 3I4ME 3GTJE 5IYCE 2R7ZE 4A3DE 5M3FE 3M4OE 1EIKA 1DZFA 2NVTE 4A93E 2Y0SH 4A3CE 2B63E 1Y1WE 1I3QE 4QIWH 5IYDE 3HOYE 1Y1VE 3PO2E 5FLME 2PMZH 1SFOE 5C44E 1TWFE 4A3EE 3M3YE 3GTPE 3PO3E 1R9TE 3S1QE 3CQZE 5IP9E 3H0GE 4BY7E 5C4XE 4A3ME 3GTLE 3K7AE 4BBSE 1TWGE 5M5YE 4C2ME 2JA8E 2YU9E 3HOXE
chains in the Genus database with same CATH superfamily
3H0GF 3S15E 4A3GE 2BE5E 4XSXE 3WODE 1K83E 4BY7F 5C4XF 4A3MF 4Q5SE 3S1ME 3GTLF 3K7AF 2VUME 4BBSF 1TWGF 3GTKE 2WB1H 4C2MF 5M5YF 2NVYE 4LK0E 2JA8F 4KMUE 2YU9F 3HOXF 3HOUE 3S15F 4A3GF 2PMZK 5C4JE 1K83F 4LJZE 5TMFE 5TMCE 3S1MF 2A6HE 4MEYE 3HOWE 3HOZE 4G7HE 4XSZE 3GTKF 2NVYF 4Y52E 3FKIE 4LLGE 1I50E 3HOUF 4YG2E 1TWCE 5M3ME 3S16E 5C4JF 2O5IE 3S1RE 4AYBH 5FJ8E 2JA7E 4A3BE 3HOWF 3S1NE 3HKZH 3HOZF 4LK1E 4A3LE 3RZOE 4Y52F 3S17E 3FKIF 1I50F 3H3VF 3I4NE 1TWCF 4X6AE 5M3MF 3S16F 2E2JE 5BYHE 3S1RF 5FJ8F 2JA5E 2NVQE 2JA7F 4A3BF 2A6EE 4YFKE 3S1NF 1TWAE 4A3JE 4A3LF 3RZOF 1WCME 2A69E 3S17F 5C3EE 4XLNE 4MQ9E 4C3HE 3S2HE 2E2HE 3I4NF 2O5JE 4X6AF 5E17E 2E2JF 5IP7E 4A3IE 2JA5F 2NVQF 5D4CE 1TWAF 1TWHE 4A3JF 5E18E 2Y0SI 1WCMF 4BBRE 2R93E 3RZDE 5C3EF 4C3HF 3S2HF 2E2HF 1HQME 5IP7F 3HOVE 4A3IF 5IYBE 4BY1E 1ZYRE 4OIPE 1TWHF 3GTQE 4AYBK 4BBRF 4BXXE 3RZDF 2R93F 1YNNK 3HKZK 4C3JE 5M5XE 4Y7NE 1I6HE 2R92E 4OIRE 3EQLE 3GTGE 3HOVF 4BY1F 5IYBF 5IPLE 5M5WE 3GTQF 2NVXE 4C3IE 2E2IE 3GTOE 2KRXA 4BXXF 2JA6E 4A3FE 4C3JF 5M5XF 4A3KE 4Y7NF 1I6HF 2R92F 3GTME 3GTGF 4YFNE 5M5WF 3S14E 2NVXF 4Q4ZE 4OIOE 2WAQH 3S2DE 4C3IF 3I4ME 3GTJE 2E2IF 3GTOF 2JA6F 5IYCE 2R7ZE 4A3DE 5M3FE 2A68E 4A3FF 3M4OE 4A3KF 4GZYE 3GTMF 1EIKA 1DZFA 2NVTE 4A93E 2Y0SH 4A3CE 2B63E 3H3VG 3S14F 3S2DF 3I4MF 4JK1E 3GTJF 5IYCF 2R7ZF 4A3DF 1YNJK 5M3FF 3M4OF 1Y1WE 1I3QE 3DXJE 4QIWH 2PPBE 5IYDE 1SMYE 2CW0E 2NVTF 4QIWK 4A93F 2WB1I 4A3CF 2B63F 1IW7E 4KN7E 4G7ZE 3HOYE 1Y1VE 3PO2E 5D4DE 1Y1WF 1I3QF 4ZH4E 5FLME 2PMZH 1SFOE 5IYDF 5C44E 1I6VE 1TWFE 4A3EE 3M3YE 3GTPE 4OINE 2VUMF 3PO3E 1R9TE 3S1QE 3CQZE 4KN4E 1Y1VF 4MEXE 3PO2F 3HOYF 5IP9F 2WAQK 5FLMF 1SFOF 5C44F 4XLPE 1TWFF 4A3EF 5D4EE 5IP9E 3M3YF 3H0GE 1QKLA 3GTPF 3PO3F 1R9TF 4BY7E 5C4XE 4A3ME 3CQZF 3S1QF 3GTLE 3K7AE 4OIQE 4BBSE 4YFXE 1TWGE 5M5YE 4C2ME 2JA8E 2YU9E 4G7OE 3HOXE
chains in the Genus database with same CATH topology
3S15E 4A3GE 1K83E 3S1ME 2VUME 3GTKE 2WB1H 2NVYE 3HOUE 5C4JE 3HOWE 3HOZE 4Y52E 3FKIE 1I50E 1TWCE 5M3ME 3S16E 3S1RE 4AYBH 5FJ8E 2JA7E 4A3BE 3S1NE 3HKZH 4A3LE 3RZOE 3S17E 3H3VF 3I4NE 4X6AE 2E2JE 2JA5E 2NVQE 1TWAE 4A3JE 1WCME 5C3EE 4C3HE 3S2HE 2E2HE 5IP7E 4A3IE 1TWHE 4BBRE 2R93E 3RZDE 3HOVE 5IYBE 4BY1E 3GTQE 4BXXE 4C3JE 5M5XE 4Y7NE 1I6HE 2R92E 3GTGE 5M5WE 2NVXE 4C3IE 2E2IE 3GTOE 2JA6E 4A3FE 4A3KE 3GTME 3S14E 2WAQH 3S2DE 3I4ME 3GTJE 5IYCE 2R7ZE 4A3DE 5M3FE 3M4OE 1EIKA 1DZFA 2NVTE 4A93E 2Y0SH 4A3CE 2B63E 1Y1WE 1I3QE 4QIWH 5IYDE 3HOYE 1Y1VE 3PO2E 5FLME 2PMZH 1SFOE 5C44E 1TWFE 4A3EE 3M3YE 3GTPE 3PO3E 1R9TE 3S1QE 3CQZE 5IP9E 3H0GE 4BY7E 5C4XE 4A3ME 3GTLE 3K7AE 4BBSE 1TWGE 5M5YE 4C2ME 2JA8E 2YU9E 3HOXE
chains in the Genus database with same CATH homology


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