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


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