3S2HE

Rna polymerase ii initiation complex with a 6-nt rna containing a 2[prime]-iodo atp
Total Genus 58
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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
58
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 Initiation complex structure and promoter proofreading.
pubmed doi rcsb
molecule tags Transcription/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 58
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2011-05-16

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 3s2hE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 3s2hE02
4A3JE 4A3IE 3PO3E 1TWAE 4A3ME 2NVTE 4X6AE 3I4ME 5M5XE 1Y1VE 4AYBH 5M3FE 1TWFE 4A3FE 3GTPE 3H0GE 1SFOE 1R9TE 3GTJE 2JA5E 3HOVE 5IYCE 1WCME 5FJ8E 3HKZH 1DZFA 3S17E 4A3GE 2R7ZE 3PO2E 4C3HE 5M5WE 2R93E 4A3LE 2JA6E 4Y7NE 3GTKE 3HOZE 3GTLE 5FLME 4BBSE 3CQZE 2JA7E 3S15E 1I50E 3FKIE 4Y52E 5C44E 3S14E 2PMZH 1TWGE 3S1RE 2Y0SH 2E2JE 3S2DE 4BY1E 4BXXE 3M3YE 3HOXE 3GTQE 2WB1H 3RZOE 1EIKA 2E2HE 3HOUE 4A3EE 2JA8E 2VUME 5IYDE 2NVYE 3S2HE 3RZDE 3S16E 5M3ME 1I6HE 4A3DE 4A3BE 1I3QE 2R92E 1Y1WE 5IYBE 3S1QE 5M5YE 4C3IE 3H3VF 2WAQH 5C3EE 3S1NE 4QIWH 3GTME 4A3CE 5C4JE 2NVQE 3GTOE 2YU9E 3HOWE 4BY7E 4C2ME 2NVXE 3M4OE 5IP7E 2E2IE 2B63E 3I4NE 1K83E 1TWHE 3K7AE 4C3JE 4BBRE 1TWCE 3GTGE 3HOYE 5C4XE 3S1ME 4A3KE 4A93E 5IP9E
chains in the Genus database with same CATH superfamily
4A3JE 5IYBF 4A3MF 5D4EE 4A3IE 3PO3E 1TWAE 4KN4E 4A3JF 2PPBE 4BBSF 4A3ME 2NVTE 4MQ9E 4X6AE 3I4ME 5M5XE 1TWAF 1Y1VE 4AYBH 1Y1WF 4ZH4E 2JA6F 3GTKF 5M3FF 2R93F 4OIRE 1YNNK 2A68E 3GTLF 5M3FE 4OIQE 3GTOF 1TWFE 4A3FE 3GTPE 1QKLA 3H0GE 1SFOE 1R9TE 3RZDF 3GTJE 4BBRF 2JA5E 3HOVE 5C4JF 5IYCE 1WCME 5E18E 4A3FF 3GTPF 5FJ8E 4A3GF 2WAQK 3HKZH 1DZFA 3S17E 5IP9F 5IYDF 3GTJF 3PO2F 2A6HE 5M5WF 4A3GE 3PO3F 5IP7F 4BY7F 3S1RF 2R7ZE 3PO2E 4C3HE 5M5WE 2R93E 5TMFE 2KRXA 2PMZK 4A3LE 4C2MF 3WODE 4YFKE 2JA6E 5M5XF 2NVXF 4Y7NE 4OIOE 2R7ZF 4LJZE 3GTKE 3DXJE 2R92F 3HOZE 4BXXF 4C3JF 3HOXF 1I50F 4MEXE 3GTLE 5FLME 2B63F 4BBSE 3I4NF 1TWFF 3CQZE 2JA7E 3S15E 4LK1E 2E2HF 1I50E 5D4DE 5D4CE 3HOUF 4A93F 1WCMF 1I6VE 5IYCF 3FKIE 1IW7E 4A3IF 1HQME 4Y52E 5C44E 3S14E 2PMZH 4A3CF 1TWGE 5M3MF 3FKIF 3S2DF 3I4MF 4A3KF 2E2JF 4BY1F 3S1RE 2Y0SH 2E2JE 3S2DE 4OIPE 5TMCE 3EQLE 4AYBK 1I3QF 4KN7E 4BY1E 4C3HF 4YFNE 4C3IF 4X6AF 4BXXE 3HOZF 3M3YE 3HOXE 1R9TF 3GTQE 2WB1H 4XSXE 2E2IF 3RZOE 1YNJK 2E2HE 3HOUE 1EIKA 4A3EE 2JA8E 2VUME 3GTMF 5E17E 5IYDE 5C4XF 2NVYE 3S2HE 3RZOF 3RZDE 1SFOF 3S16E 4KMUE 2NVYF 5M3ME 1TWGF 3S2HF 1I6HE 4MEYE 3H3VG 3HOWF 4A3LF 4YG2E 1TWCF 3GTGF 5M5YF 3HOYF 4LLGE 4Q4ZE 4A3DE 4A3BE 1I3QE 2R92E 1Y1WE 5IYBE 4XSZE 3S1QE 5M5YE 4C3IE 4Q5SE 4A3BF 3H3VF 2WAQH 3HKZK 3S1NF 3M3YF 1ZYRE 4Y7NF 3S1QF 2A6EE 5C3EE 3S1NE 3H0GF 4QIWH 3GTME 4A3CE 5C44F 5C4JE 2JA5F 2JA8F 2VUMF 3HOVF 2CW0E 3S14F 4XLNE 5FJ8F 2JA7F 3S15F 2NVQE 4G7OE 3GTOE 2YU9E 2Y0SI 2O5IE 3S1MF 2NVQF 3HOWE 4JK1E 4Y52F 4BY7E 1I6HF 4A3DF 4C2ME 2NVXE 3S17F 3M4OE 2NVTF 5BYHE 2O5JE 5IP7E 1SMYE 1Y1VF 3M4OF 2WB1I 2E2IE 4GZYE 5C3EF 2B63E 3I4NE 1TWHF 3K7AF 2BE5E 1K83E 3S16F 3GTQF 4YFXE 1TWHE 3K7AE 4LK0E 4G7HE 4C3JE 1K83F 2A69E 4XLPE 4A3EF 5FLMF 4BBRE 4OINE 4QIWK 1TWCE 3GTGE 3HOYE 5C4XE 3CQZF 4G7ZE 2YU9F 3S1ME 5IPLE 4A3KE 4A93E 5IP9E
chains in the Genus database with same CATH topology
4A3JE 4A3IE 3PO3E 1TWAE 4A3ME 2NVTE 4X6AE 3I4ME 5M5XE 1Y1VE 4AYBH 5M3FE 1TWFE 4A3FE 3GTPE 3H0GE 1SFOE 1R9TE 3GTJE 2JA5E 3HOVE 5IYCE 1WCME 5FJ8E 3HKZH 1DZFA 3S17E 4A3GE 2R7ZE 3PO2E 4C3HE 5M5WE 2R93E 4A3LE 2JA6E 4Y7NE 3GTKE 3HOZE 3GTLE 5FLME 4BBSE 3CQZE 2JA7E 3S15E 1I50E 3FKIE 4Y52E 5C44E 3S14E 2PMZH 1TWGE 3S1RE 2Y0SH 2E2JE 3S2DE 4BY1E 4BXXE 3M3YE 3HOXE 3GTQE 2WB1H 3RZOE 1EIKA 2E2HE 3HOUE 4A3EE 2JA8E 2VUME 5IYDE 2NVYE 3S2HE 3RZDE 3S16E 5M3ME 1I6HE 4A3DE 4A3BE 1I3QE 2R92E 1Y1WE 5IYBE 3S1QE 5M5YE 4C3IE 3H3VF 2WAQH 5C3EE 3S1NE 4QIWH 3GTME 4A3CE 5C4JE 2NVQE 3GTOE 2YU9E 3HOWE 4BY7E 4C2ME 2NVXE 3M4OE 5IP7E 2E2IE 2B63E 3I4NE 1K83E 1TWHE 3K7AE 4C3JE 4BBRE 1TWCE 3GTGE 3HOYE 5C4XE 3S1ME 4A3KE 4A93E 5IP9E
chains in the Genus database with same CATH homology


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