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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molecule tags Transcription/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Initiation complex structure and promoter proofreading.
pubmed doi rcsb
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
2R7ZE 1I6HE 3S15E 3HOZE 2WB1H 3GTQE 2R92E 4A3KE 4A3EE 1SFOE 4A3FE 1TWAE 2NVQE 3M3YE 3H3VF 3GTGE 2VUME 3HOVE 4A3GE 3RZOE 5IYCE 1R9TE 3M4OE 4A3IE 3HOXE 1TWGE 3S2DE 4BXXE 4A3BE 5FJ8E 4C3HE 3HOWE 2PMZH 2B63E 3HOUE 2WAQH 5M3ME 3HKZH 3GTME 5C4XE 3S2HE 1TWHE 4C2ME 4Y7NE 3I4NE 3GTPE 3PO2E 4A3JE 3S1QE 1I3QE 2NVXE 2R93E 4X6AE 5C4JE 1Y1WE 3S1RE 1TWCE 3I4ME 2JA8E 3PO3E 2YU9E 3GTLE 1Y1VE 5IYBE 4C3JE 3CQZE 4A3DE 5IP7E 2E2IE 2E2JE 4A3LE 2JA5E 1K83E 5M5XE 4BY7E 3GTKE 4A93E 2NVTE 4AYBH 2Y0SH 5C44E 1DZFA 4QIWH 3S1NE 1TWFE 4A3ME 5C3EE 1EIKA 2JA7E 5IP9E 3GTOE 2E2HE 1I50E 5M5WE 3FKIE 3S16E 3RZDE 3GTJE 3S1ME 3S17E 3H0GE 5M3FE 4A3CE 4BBRE 4Y52E 2NVYE 4BY1E 5FLME 1WCME 4BBSE 3K7AE 2JA6E 4C3IE 5M5YE 3HOYE 3S14E 5IYDE
chains in the Genus database with same CATH superfamily
4ZH4E 3S2HF 2R7ZE 2NVQF 1I6HE 1TWHF 4C2MF 4Y7NF 3S1QF 3S15E 3GTPF 3HOZE 4A3JF 3PO2F 1YNJK 2R93F 4X6AF 5C4JF 2WB1H 1Y1WF 5IYCF 3S1RF 3I4MF 3GTQE 4G7HE 2R92E 2JA8F 4OIOE 2YU9F 3PO3F 4A3KE 4A3EE 1SFOE 3HOXF 4A3FE 3GTLF 1YNNK 4XSZE 1TWAE 1SMYE 1TWGF 1Y1VF 2NVQE 3M3YE 3H3VF 5IYBF 3GTGE 5D4CE 4C3JF 2VUME 3CQZF 4A3DF 3HOVE 5E18E 2A6HE 4AYBK 4A3GE 5IP7F 2PPBE 2E2IF 3RZOE 5IYCE 1R9TE 3M4OE 1IW7E 2E2JF 4A3LF 4A3IE 4OIQE 2JA5F 3HOXE 2O5IE 1K83F 4MQ9E 5M5XF 3I4NF 1TWGE 4BY7F 3GTKF 1I3QF 3DXJE 5D4EE 3S2DE 2NVTF 4BXXE 4A93F 4A3BE 2NVXF 2Y0SI 5C44F 5FJ8E 2CW0E 1TWCF 4C3HE 3HOWE 5D4DE 2PMZH 2B63E 3HOUE 2WAQH 5M3ME 3HKZH 4LLGE 3S1NF 4MEXE 1TWFF 3WODE 3GTME 5C4XE 4YFNE 4A3MF 5C3EF 3S2HE 1TWHE 4C2ME 4Y7NE 3I4NE 3GTPE 3PO2E 4A3JE 3S1QE 4G7ZE 1I3QE 2E2HF 1HQME 3GTOF 4GZYE 4OIRE 2A6EE 2NVXE 4LK1E 2R93E 4X6AE 3S16F 2O5JE 5C4JE 3GTJF 3S1MF 1Y1WE 3H0GF 3S1RE 1TWCE 3I4ME 4KN4E 4BBRF 2JA8E 1QKLA 3PO3E 2YU9E 4OIPE 4Y52F 4BY1F 3GTLE 1WCMF 2A68E 3K7AF 4BBSF 5E17E 2JA6F 5TMCE 1Y1VE 4C3IF 2KRXA 5M5YF 3S14F 5IYBE 3EQLE 5BYHE 2PMZK 4C3JE 2WAQK 3CQZE 5IYDF 4A3DE 5IP7E 2R7ZF 1I6HF 2E2IE 3S15F 3HOZF 2E2JE 4A3LE 5IPLE 2JA5E 1K83E 2WB1I 4YFXE 5M5XE 2JA7F 3GTMF 3GTQF 4BY7E 3GTKE 4KMUE 5IP9F 4A93E 1I50F 1ZYRE 2NVTE 5M5WF 4A3KF 4AYBH 4A3EF 2A69E 4A3FF 3FKIF 1SFOF 1TWAF 5C44E 2Y0SH 3RZDF 3S17F 3M3YF 4OINE 1DZFA 4QIWH 5M3FF 4JK1E 3GTGF 4KN7E 4A3CF 3H3VG 2VUMF 3S1NE 3HOVF 1I6VE 2NVYF 1TWFE 4MEYE 5FLMF 4A3GF 4A3ME 5C3EE 3HOYF 3RZOF 1EIKA 2JA7E 4Q5SE 1R9TF 3M4OF 5IP9E 3GTOE 2E2HE 4A3IF 4G7OE 1I50E 3HKZK 5M5WE 4XLPE 3FKIE 3S16E 3RZDE 3GTJE 3S1ME 3S17E 4LJZE 3H0GE 2BE5E 5TMFE 5M3FE 4A3CE 3S2DF 4BXXF 4BBRE 4Q4ZE 4YFKE 4XLNE 4A3BF 4LK0E 4Y52E 2NVYE 4BY1E 5FLME 1WCME 4BBSE 3K7AE 4YG2E 5FJ8F 4XSXE 2JA6E 4C3IE 5M5YE 3HOYE 3S14E 4C3HF 2B63F 2R92F 3HOUF 5M3MF 3HOWF 4QIWK 5IYDE 5C4XF
chains in the Genus database with same CATH topology
2R7ZE 1I6HE 3S15E 3HOZE 2WB1H 3GTQE 2R92E 4A3KE 4A3EE 1SFOE 4A3FE 1TWAE 2NVQE 3M3YE 3H3VF 3GTGE 2VUME 3HOVE 4A3GE 3RZOE 5IYCE 1R9TE 3M4OE 4A3IE 3HOXE 1TWGE 3S2DE 4BXXE 4A3BE 5FJ8E 4C3HE 3HOWE 2PMZH 2B63E 3HOUE 2WAQH 5M3ME 3HKZH 3GTME 5C4XE 3S2HE 1TWHE 4C2ME 4Y7NE 3I4NE 3GTPE 3PO2E 4A3JE 3S1QE 1I3QE 2NVXE 2R93E 4X6AE 5C4JE 1Y1WE 3S1RE 1TWCE 3I4ME 2JA8E 3PO3E 2YU9E 3GTLE 1Y1VE 5IYBE 4C3JE 3CQZE 4A3DE 5IP7E 2E2IE 2E2JE 4A3LE 2JA5E 1K83E 5M5XE 4BY7E 3GTKE 4A93E 2NVTE 4AYBH 2Y0SH 5C44E 1DZFA 4QIWH 3S1NE 1TWFE 4A3ME 5C3EE 1EIKA 2JA7E 5IP9E 3GTOE 2E2HE 1I50E 5M5WE 3FKIE 3S16E 3RZDE 3GTJE 3S1ME 3S17E 3H0GE 5M3FE 4A3CE 4BBRE 4Y52E 2NVYE 4BY1E 5FLME 1WCME 4BBSE 3K7AE 2JA6E 4C3IE 5M5YE 3HOYE 3S14E 5IYDE
chains in the Genus database with same CATH homology


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