5C4XE

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
Total Genus 54
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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
54
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 Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
pubmed doi rcsb
source organism Saccharomyces cerevisiae (strain atcc 204508 / s288c)
molecule tags Transferase/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 54
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2015-06-18

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 5c4xE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 5c4xE02
3K7AE 5M5YE 4BXXE 5IP7E 4C2ME 3S2DE 3S14E 3S1NE 4A3JE 4A93E 3HOXE 3GTKE 3RZDE 3RZOE 5IYCE 2JA7E 4A3LE 3PO3E 3CQZE 2WAQH 5C3EE 3I4NE 2R92E 3GTQE 2PMZH 2WB1H 4QIWH 2E2IE 4A3DE 4Y7NE 2NVXE 3S16E 1DZFA 3I4ME 1TWAE 3M4OE 4A3KE 3S2HE 1I6HE 3GTME 3HOZE 5IP9E 4AYBH 4C3JE 2JA5E 4C3HE 1Y1WE 2YU9E 1K83E 2E2JE 3GTJE 2JA8E 4A3EE 2R7ZE 3FKIE 5IYBE 2JA6E 2B63E 5M5WE 3HOWE 1TWGE 4A3GE 2R93E 1TWFE 1WCME 1I3QE 5C4XE 4A3BE 1R9TE 3GTGE 4BY7E 4A3CE 3H3VF 1Y1VE 3S15E 3S1RE 3GTPE 2NVTE 2E2HE 3GTLE 2NVQE 5M3ME 2VUME 4X6AE 5IYDE 3S1ME 4A3ME 1SFOE 2NVYE 5FLME 4Y52E 5C4JE 5M5XE 3S1QE 1TWHE 3HOVE 1I50E 3HKZH 3H0GE 3HOUE 2Y0SH 3PO2E 3M3YE 5M3FE 3HOYE 4A3FE 3GTOE 4A3IE 1EIKA 4BBSE 5FJ8E 4BY1E 4BBRE 3S17E 5C44E 1TWCE 4C3IE
chains in the Genus database with same CATH superfamily
1YNNK 3K7AE 5M5YE 3I4MF 3S1NF 4BXXE 4A93F 4G7OE 5IP7E 3S1MF 2R93F 3K7AF 4C3IF 4A3DF 4C2ME 2O5JE 4YFKE 3S2DE 3S14E 3S1NE 4A3JE 4A93E 3GTQF 3HOXE 2JA8F 2NVQF 4MEXE 3GTLF 2PMZK 3GTKE 3DXJE 1QKLA 1K83F 4MQ9E 3RZDE 3RZOF 4C3HF 1Y1WF 5BYHE 4A3FF 3RZOE 5IYCE 4LK0E 2PPBE 4XSZE 4LK1E 1I6HF 2JA7E 4A3LE 1I50F 3PO3E 4XLPE 1SMYE 3CQZE 5D4EE 2WAQH 1R9TF 5C3EE 3I4NE 2R92E 3GTQE 2PMZH 3HOVF 2WB1H 1WCMF 4QIWH 5M5XF 5E18E 2R7ZF 2E2IE 2A68E 3S14F 5IYDF 5M3MF 4A3DE 4LLGE 4X6AF 1IW7E 3CQZF 4OIPE 5TMCE 4Y7NE 2NVXE 3S16E 1DZFA 4A3MF 3I4ME 5M5YF 1TWAE 4A3LF 3M4OE 2E2JF 4A3KE 3H3VG 4OIQE 2A6HE 3GTMF 4OINE 3HOZF 3S2HE 1I6HE 2CW0E 5IP9F 4LJZE 3GTME 3HOZE 3S1RF 5IYCF 5IP9E 1HQME 3S15F 4AYBH 3GTGF 4C3JE 2WB1I 3S2HF 2JA5E 4C3HE 1Y1WE 1I6VE 3HOXF 2O5IE 4A3CF 4G7ZE 2YU9E 1K83E 4YG2E 3GTKF 2E2JE 5M5WF 3HOUF 2NVYF 3GTJE 4ZH4E 2B63F 3EQLE 2JA8E 3HOWF 1TWAF 5D4DE 1I3QF 3FKIF 4A3EE 1TWFF 3HKZK 5IYBF 1SFOF 2R7ZE 1TWGF 3FKIE 5IYBE 2JA6E 1ZYRE 2KRXA 4G7HE 4KN4E 2B63E 3GTJF 2JA6F 5M5WE 3HOWE 1TWGE 4A3GE 4JK1E 5IP7F 5C44F 2R93E 4OIRE 1TWFE 1WCME 4BXXF 1I3QE 4XSXE 5C4XE 2VUMF 4A3BE 1R9TE 1YNJK 4QIWK 4BY1F 3GTGE 2E2HF 5IPLE 4BY7E 1TWCF 2NVTF 2YU9F 4A3CE 5D4CE 5TMFE 1Y1VF 4BBRF 2JA7F 4Q5SE 3H3VF 1Y1VE 3S15E 3M3YF 5FJ8F 3WODE 3S1RE 3GTPE 3RZDF 4BBSF 2NVTE 2BE5E 4KMUE 4YFNE 4GZYE 2A69E 3H0GF 2A6EE 3PO2F 4A3KF 4A3GF 2E2HE 4Y52F 3GTLE 3S2DF 2NVQE 5M3ME 2VUME 4X6AE 5IYDE 5C4XF 3S1QF 4Q4ZE 4A3JF 3S1ME 4A3ME 1SFOE 4Y7NF 2NVXF 3S16F 5FLMF 4C2MF 5C3EF 2NVYE 5FLME 4Y52E 4OIOE 2E2IF 5C4JE 5M5XE 3S17F 4A3EF 3S1QE 1TWHE 4MEYE 3HOVE 2R92F 1I50E 3HKZH 3H0GE 3I4NF 3HOUE 3PO3F 4AYBK 4XLNE 2Y0SH 3PO2E 3M3YE 5M3FE 3HOYE 4A3FE 2JA5F 4C3JF 3GTOE 4A3IE 1EIKA 4BBSE 2Y0SI 3GTPF 5FJ8E 4A3IF 3GTOF 4BY1E 4A3BF 4BBRE 4YFXE 5M3FF 3HOYF 5E17E 3S17E 5C44E 1TWCE 4BY7F 5C4JF 4KN7E 3M4OF 1TWHF 4C3IE 2WAQK
chains in the Genus database with same CATH topology
3K7AE 5M5YE 4BXXE 5IP7E 4C2ME 3S2DE 3S14E 3S1NE 4A3JE 4A93E 3HOXE 3GTKE 3RZDE 3RZOE 5IYCE 2JA7E 4A3LE 3PO3E 3CQZE 2WAQH 5C3EE 3I4NE 2R92E 3GTQE 2PMZH 2WB1H 4QIWH 2E2IE 4A3DE 4Y7NE 2NVXE 3S16E 1DZFA 3I4ME 1TWAE 3M4OE 4A3KE 3S2HE 1I6HE 3GTME 3HOZE 5IP9E 4AYBH 4C3JE 2JA5E 4C3HE 1Y1WE 2YU9E 1K83E 2E2JE 3GTJE 2JA8E 4A3EE 2R7ZE 3FKIE 5IYBE 2JA6E 2B63E 5M5WE 3HOWE 1TWGE 4A3GE 2R93E 1TWFE 1WCME 1I3QE 5C4XE 4A3BE 1R9TE 3GTGE 4BY7E 4A3CE 3H3VF 1Y1VE 3S15E 3S1RE 3GTPE 2NVTE 2E2HE 3GTLE 2NVQE 5M3ME 2VUME 4X6AE 5IYDE 3S1ME 4A3ME 1SFOE 2NVYE 5FLME 4Y52E 5C4JE 5M5XE 3S1QE 1TWHE 3HOVE 1I50E 3HKZH 3H0GE 3HOUE 2Y0SH 3PO2E 3M3YE 5M3FE 3HOYE 4A3FE 3GTOE 4A3IE 1EIKA 4BBSE 5FJ8E 4BY1E 4BBRE 3S17E 5C44E 1TWCE 4C3IE
chains in the Genus database with same CATH homology


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