3RZDE

Rna polymerase ii initiation complex with a 5-nt rna
Total Genus 59
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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
59
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
publication title Initiation complex structure and promoter proofreading.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 59
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2011-05-11

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 3rzdE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 3rzdE02
4A3GE 1I3QE 4BBRE 3HOUE 4BY1E 3S2DE 3H0GE 1EIKA 3CQZE 3HOWE 3S16E 3GTGE 4QIWH 3PO3E 2NVXE 4A3ME 2JA8E 3I4NE 2R92E 1WCME 3PO2E 4Y7NE 1I50E 3FKIE 5IP7E 4A3CE 3S1RE 2R7ZE 3H3VF 5C44E 2WB1H 5FLME 2E2JE 1TWHE 4C2ME 2JA6E 3HKZH 5FJ8E 3GTJE 4AYBH 5M3ME 4C3JE 4A3JE 3S1NE 2JA7E 2NVQE 2E2IE 2NVYE 2JA5E 4Y52E 1TWCE 4A3KE 1K83E 5M5XE 4C3IE 5C4XE 3K7AE 4BY7E 4BXXE 2B63E 3HOVE 5IYBE 3GTQE 1TWFE 3I4ME 3GTLE 4A3BE 5M5YE 2E2HE 5C3EE 3RZDE 3M4OE 5C4JE 4A3DE 5IYDE 4X6AE 4A3LE 2Y0SH 1R9TE 4BBSE 3GTKE 3GTME 5IP9E 2VUME 3S14E 1I6HE 3S15E 1Y1VE 2YU9E 2R93E 2PMZH 1SFOE 1DZFA 1TWGE 4C3HE 2WAQH 1Y1WE 5M5WE 2NVTE 3HOXE 3S1ME 3S2HE 3HOZE 4A3EE 5IYCE 4A3IE 3S17E 3S1QE 4A93E 3GTOE 1TWAE 3M3YE 3RZOE 4A3FE 3HOYE 3GTPE 5M3FE
chains in the Genus database with same CATH superfamily
4A3GE 1SMYE 1I3QE 5IYDF 4BBRE 5C4JF 4X6AF 4A3LF 4BBSF 3HOUE 4QIWK 3GTKF 4BY1E 3GTMF 3S2DE 4Q4ZE 5IP9F 3H0GE 3DXJE 3CQZE 3HOWE 3S16E 4A3FF 4MEXE 2VUMF 1I6HF 3GTGE 4OIQE 3HOYF 3S15F 4G7OE 4YFNE 4Q5SE 4QIWH 2PPBE 2YU9F 2R93F 1SFOF 4BY1F 3PO3E 4XLPE 2NVXE 4A3ME 2JA8E 3I4NE 2R92E 3H0GF 1TWGF 1WCME 2CW0E 3PO2E 2Y0SI 1Y1WF 4Y7NE 4YFKE 2NVTF 1I50E 4LJZE 3HKZK 3HOXF 3S1MF 2A68E 3FKIE 5IP7E 4A3CE 3HOZF 4A3EF 3S1RE 3S2HF 2R7ZE 3H3VF 5C44E 2WB1H 5IYCF 5FLME 2R92F 2E2JE 4A3IF 5TMCE 3S17F 1TWHE 2KRXA 4C2ME 2JA6E 4YG2E 3S1QF 4A93F 3HKZH 4Y7NF 3GTOF 1I50F 4XLNE 5FJ8E 1TWAF 4OIPE 3GTJE 4AYBH 3M3YF 3RZOF 5M3ME 3GTPF 4C3JE 4LK1E 5M3FF 4A3JE 3S14F 4A3GF 1I3QF 1TWHF 3S1NE 4BBRF 2JA7E 2NVQE 2E2IE 3HOUF 2O5IE 3S2DF 4GZYE 3GTJF 2NVYE 3CQZF 3HOWF 3S16F 3GTGF 5IPLE 1YNNK 2JA5E 4Y52E 1TWCE 3EQLE 1EIKA 4A3KE 2NVQF 1K83E 2E2IF 2WB1I 3PO3F 5M5XE 4C3IE 5C4XE 4KN7E 2NVXF 3K7AE 4BY7E 4BXXE 1ZYRE 4A3MF 4G7HE 2JA8F 3I4NF 2B63E 3HOVE 1WCMF 5IYBE 3GTQE 3PO2F 1TWFE 3I4ME 1TWCF 3GTLE 4MQ9E 4OIRE 1K83F 1YNJK 4A3BE 3FKIF 5IP7F 4A3CF 4LK0E 3S1RF 5M5YE 2E2HE 5C3EE 5C44F 3K7AF 2R7ZF 5FLMF 2A6EE 1QKLA 4MEYE 2E2JF 3HOVF 3H3VG 5IYBF 3RZDE 4C2MF 2JA6F 3M4OE 5BYHE 3GTLF 5C4JE 4A3DE 5IYDE 4KN4E 4AYBK 4X6AE 4XSXE 5FJ8F 4A3LE 4ZH4E 2Y0SH 1R9TE 4BBSE 2BE5E 5M5YF 5D4DE 2O5JE 3GTKE 4XSZE 2PMZK 5M3MF 3GTME 4C3JF 4A3JF 3WODE 5IP9E 2VUME 3S14E 3S1NF 2JA7F 5TMFE 1I6HE 1HQME 3S15E 4A3DF 2A6HE 1Y1VE 2YU9E 2R93E 2PMZH 2WAQK 1R9TF 2NVYF 1SFOE 4OIOE 5E17E 4OINE 4KMUE 4Y52F 1DZFA 2JA5F 1TWGE 4YFXE 4C3HE 5D4EE 4A3KF 2WAQH 1Y1WE 5M5WE 1Y1VF 4C3IF 2NVTE 5M5XF 5C4XF 4BY7F 3HOXE 3S1ME 3S2HE 4BXXF 1I6VE 3HOZE 4A3EE 4LLGE 5D4CE 2B63F 3GTQF 5IYCE 1IW7E 1TWFF 3I4MF 2A69E 4C3HF 4A3IE 3S17E 3S1QE 4A93E 3GTOE 5M5WF 4G7ZE 2E2HF 5C3EF 4A3BF 5E18E 1TWAE 4JK1E 3M3YE 3RZOE 3RZDF 4A3FE 3HOYE 3GTPE 3M4OF 5M3FE
chains in the Genus database with same CATH topology
4A3GE 1I3QE 4BBRE 3HOUE 4BY1E 3S2DE 3H0GE 1EIKA 3CQZE 3HOWE 3S16E 3GTGE 4QIWH 3PO3E 2NVXE 4A3ME 2JA8E 3I4NE 2R92E 1WCME 3PO2E 4Y7NE 1I50E 3FKIE 5IP7E 4A3CE 3S1RE 2R7ZE 3H3VF 5C44E 2WB1H 5FLME 2E2JE 1TWHE 4C2ME 2JA6E 3HKZH 5FJ8E 3GTJE 4AYBH 5M3ME 4C3JE 4A3JE 3S1NE 2JA7E 2NVQE 2E2IE 2NVYE 2JA5E 4Y52E 1TWCE 4A3KE 1K83E 5M5XE 4C3IE 5C4XE 3K7AE 4BY7E 4BXXE 2B63E 3HOVE 5IYBE 3GTQE 1TWFE 3I4ME 3GTLE 4A3BE 5M5YE 2E2HE 5C3EE 3RZDE 3M4OE 5C4JE 4A3DE 5IYDE 4X6AE 4A3LE 2Y0SH 1R9TE 4BBSE 3GTKE 3GTME 5IP9E 2VUME 3S14E 1I6HE 3S15E 1Y1VE 2YU9E 2R93E 2PMZH 1SFOE 1DZFA 1TWGE 4C3HE 2WAQH 1Y1WE 5M5WE 2NVTE 3HOXE 3S1ME 3S2HE 3HOZE 4A3EE 5IYCE 4A3IE 3S17E 3S1QE 4A93E 3GTOE 1TWAE 3M3YE 3RZOE 4A3FE 3HOYE 3GTPE 5M3FE
chains in the Genus database with same CATH homology


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