3S1QE

Rna polymerase ii initiation complex with a 5-nt 3'-deoxy rna soaked with atp
Total Genus 61
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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
61
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 61
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 3s1qE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 3s1qE02
5C44E 5IYDE 2WB1H 4C3JE 5IP7E 3HOVE 3S1ME 4C3IE 4A3IE 3PO2E 2R7ZE 1TWCE 4Y7NE 4A3DE 3HKZH 2NVXE 3S1QE 1TWGE 2B63E 2Y0SH 4C3HE 4Y52E 2VUME 3S1RE 2JA5E 2E2JE 3GTQE 3I4NE 5M3ME 3S15E 3S2DE 3GTOE 3K7AE 3H0GE 1TWHE 5C3EE 5C4JE 3S16E 2NVYE 4BY7E 1TWFE 5IYCE 3GTPE 4AYBH 2NVQE 4A3ME 5C4XE 1DZFA 3I4ME 4A3GE 5M5XE 4A3BE 3S17E 3RZOE 2R93E 3HOZE 3GTJE 2YU9E 3M3YE 3GTME 1I3QE 3HOWE 2JA7E 4BBRE 4A3JE 2JA6E 1R9TE 4A93E 1Y1VE 5IYBE 3FKIE 3S2HE 4A3FE 3PO3E 5M5WE 1I6HE 2R92E 5IP9E 4BXXE 4A3CE 2PMZH 2E2HE 3HOUE 4X6AE 1I50E 4A3EE 3RZDE 2NVTE 1K83E 5FJ8E 5M5YE 5M3FE 3HOXE 5FLME 3S1NE 2E2IE 3GTGE 4A3KE 3GTKE 4BBSE 4BY1E 2JA8E 1SFOE 1WCME 2WAQH 3GTLE 3S14E 4A3LE 1EIKA 4C2ME 1Y1WE 3M4OE 3HOYE 3CQZE 1TWAE 3H3VF 4QIWH
chains in the Genus database with same CATH superfamily
5C44E 5D4EE 1YNNK 1I6HF 2R92F 4G7ZE 4A3EF 5IYDE 4YFXE 1I50F 4A3FF 3PO3F 1Y1VF 4LK0E 2A68E 2WB1H 4LK1E 5IYBF 4MEXE 3HOUF 3S2HF 4C3JE 5IP7E 3HOVE 3S1ME 1HQME 2BE5E 2E2HF 4A3JF 4AYBK 4C3IE 2JA6F 4BXXF 5IP9F 4A3CF 4OIPE 4A3IE 3WODE 5D4DE 4OINE 3PO2E 5M5WF 2R7ZE 1I3QF 1TWCE 1ZYRE 2PMZK 3FKIF 4Y7NE 4XLNE 4A93F 4A3DE 3HKZH 1R9TF 2NVXE 3GTMF 2YU9F 3S1QE 4BBRF 5TMCE 3RZOF 1TWGE 2B63E 2Y0SH 2JA7F 3S17F 4C3HE 4Y52E 2VUME 2KRXA 5M5XF 3S1RE 2JA5E 4A3BF 2E2JE 3GTQE 4LJZE 4Q5SE 3HOWF 4XLPE 3I4MF 5C4XF 3I4NE 4A3MF 1YNJK 2O5IE 2A6EE 2NVQF 4GZYE 5M3ME 3GTJF 4OIRE 3S15E 3S2DE 3HOZF 3GTOE 3M3YF 2R93F 4LLGE 3K7AE 4BY7F 3H0GE 4YG2E 1TWHE 4A3GF 5C3EE 5C4JE 3S16E 5C3EF 1TWHF 2NVYE 4BY7E 3K7AF 1TWFE 5IYCE 3GTPF 3GTPE 5IYCF 1TWFF 2NVQE 4AYBH 4KN4E 4G7OE 2NVYF 4ZH4E 4A3ME 2Y0SI 3I4NF 5C4XE 1DZFA 3S16F 3I4ME 5C4JF 1I6VE 4A3GE 2CW0E 3H0GF 5M5XE 4Y52F 4A3BE 4C3HF 3S17E 2A69E 2WB1I 3GTOF 3RZOE 2R93E 3HOZE 2PPBE 3S2DF 3GTJE 2YU9E 3M3YE 5M3MF 3S15F 3GTME 2NVXF 3S1QF 4A3DF 1TWCF 1I3QE 4XSXE 3HOWE 4OIOE 3GTQF 2E2JF 3S1RF 2JA5F 2VUMF 4A3IF 2JA7E 1TWGF 2B63F 4BBRE 4C3IF 4A3JE 2JA6E 4OIQE 3S1MF 1R9TE 4C3JF 4YFNE 5IP7F 4A93E 4Y7NF 1Y1VE 5IYBE 3FKIE 3S2HE 4A3FE 2R7ZF 3PO3E 3HKZK 5M5WE 5IYDF 3PO2F 1I6HE 2R92E 5C44F 5D4CE 5IPLE 5IP9E 4BXXE 4A3CE 2PMZH 2E2HE 3HOVF 3HOUE 3CQZF 3M4OF 3HOYF 1SMYE 5BYHE 4X6AE 1I50E 4A3EE 4A3LF 3RZDE 2NVTE 1K83E 5FJ8E 2A6HE 3EQLE 3GTLF 3S14F 5M5YE 1WCMF 5M3FE 4Q4ZE 3HOXE 4KMUE 1SFOF 5FLME 1TWAF 3S1NE 4XSZE 2E2IE 4G7HE 1Y1WF 3H3VG 4C2MF 2WAQK 3GTKF 3GTGE 4KN7E 4A3KE 3GTKE 4BBSE 4MQ9E 4BY1E 4JK1E 4QIWK 2JA8E 4YFKE 2O5JE 3DXJE 5TMFE 5E18E 2JA8F 5FLMF 4BY1F 1SFOE 3HOXF 5M3FF 1WCME 2WAQH 4BBSF 1QKLA 4A3KF 5FJ8F 3GTLE 3S14E 1K83F 4A3LE 3RZDF 2NVTF 3GTGF 1EIKA 4MEYE 4C2ME 4X6AF 1Y1WE 3M4OE 3HOYE 3CQZE 2E2IF 3S1NF 1TWAE 5E17E 1IW7E 3H3VF 5M5YF 4QIWH
chains in the Genus database with same CATH topology
5C44E 5IYDE 2WB1H 4C3JE 5IP7E 3HOVE 3S1ME 4C3IE 4A3IE 3PO2E 2R7ZE 1TWCE 4Y7NE 4A3DE 3HKZH 2NVXE 3S1QE 1TWGE 2B63E 2Y0SH 4C3HE 4Y52E 2VUME 3S1RE 2JA5E 2E2JE 3GTQE 3I4NE 5M3ME 3S15E 3S2DE 3GTOE 3K7AE 3H0GE 1TWHE 5C3EE 5C4JE 3S16E 2NVYE 4BY7E 1TWFE 5IYCE 3GTPE 4AYBH 2NVQE 4A3ME 5C4XE 1DZFA 3I4ME 4A3GE 5M5XE 4A3BE 3S17E 3RZOE 2R93E 3HOZE 3GTJE 2YU9E 3M3YE 3GTME 1I3QE 3HOWE 2JA7E 4BBRE 4A3JE 2JA6E 1R9TE 4A93E 1Y1VE 5IYBE 3FKIE 3S2HE 4A3FE 3PO3E 5M5WE 1I6HE 2R92E 5IP9E 4BXXE 4A3CE 2PMZH 2E2HE 3HOUE 4X6AE 1I50E 4A3EE 3RZDE 2NVTE 1K83E 5FJ8E 5M5YE 5M3FE 3HOXE 5FLME 3S1NE 2E2IE 3GTGE 4A3KE 3GTKE 4BBSE 4BY1E 2JA8E 1SFOE 1WCME 2WAQH 3GTLE 3S14E 4A3LE 1EIKA 4C2ME 1Y1WE 3M4OE 3HOYE 3CQZE 1TWAE 3H3VF 4QIWH
chains in the Genus database with same CATH homology


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