5FLME

Structure of transcribing mammalian rna polymerase ii
Total Genus 41
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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
41
sequence length
209
structure length
209
Chain Sequence
DDEEETYRLWKIRKTIMQLCHDRGYLVTQDGLDQTLEEFKAQFGGKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ
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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 Structure of Transcribing Mammalian RNA Polymerase II
pubmed doi rcsb
molecule tags Transcription
molecule keywords DNA-DIRECTED RNA POLYMERASE
total genus 41
structure length 209
sequence length 209
ec nomenclature
pdb deposition date 2015-10-26

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 5flmE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 5flmE02
5C3EE 4A3DE 3GTJE 3S2DE 1WCME 3M4OE 4A3ME 3S14E 1Y1WE 4A3BE 2E2IE 3S1QE 2R93E 4A3FE 2E2JE 1TWCE 3HOUE 2WAQH 5C44E 4BXXE 3S15E 4BY7E 2VUME 2JA8E 1DZFA 4X6AE 5IYDE 4A3GE 5M3FE 1K83E 3H0GE 5M5YE 1TWFE 3HOXE 5FLME 4C3JE 4A3KE 5IYBE 3GTOE 2WB1H 1TWHE 1TWGE 2B63E 3I4ME 4QIWH 4BY1E 2PMZH 3CQZE 5M3ME 3GTQE 2R7ZE 5M5XE 5C4XE 4A3IE 1SFOE 3S1ME 4C3IE 1I3QE 2JA5E 2JA6E 3I4NE 2E2HE 3PO2E 4BBSE 4A3EE 2Y0SH 3RZOE 2NVTE 3HOVE 1EIKA 3H3VF 1R9TE 1I6HE 3S1RE 5IP9E 3S2HE 1I50E 3PO3E 2R92E 4A3JE 3GTGE 4Y7NE 5IP7E 3GTME 3HOZE 4A3LE 3S16E 1TWAE 2NVXE 4C2ME 3S1NE 5C4JE 3S17E 4A93E 2NVQE 3GTKE 4BBRE 3GTPE 2YU9E 1Y1VE 4C3HE 5IYCE 3RZDE 3FKIE 3HKZH 3M3YE 4Y52E 4A3CE 5M5WE 3HOYE 3K7AE 3HOWE 3GTLE 5FJ8E 2NVYE 2JA7E 4AYBH
chains in the Genus database with same CATH superfamily
5C3EE 4A3DE 3GTJE 1Y1WF 4G7OE 3S2DE 1YNNK 2E2IF 3S1QF 1WCME 3M4OE 4A3ME 4A3FF 2B63F 2E2JF 3S14E 2PMZK 1Y1WE 4A3BE 4BY1F 2E2IE 3S1QE 2R93E 1HQME 3CQZF 4BXXF 4A3FE 2E2JE 1TWCE 5M3MF 4MQ9E 3HOUE 2WAQH 3S15F 5C44E 4X6AF 4MEYE 4BXXE 5IPLE 5IYDF 3S15E 4A3IF 3WODE 1SFOF 5M3FF 4BY7E 3S1MF 3H0GF 1YNJK 2VUME 2JA8E 1I3QF 1DZFA 4X6AE 3HOXF 5FLMF 5IYDE 4C3JF 4OIRE 3I4NF 4Q4ZE 3PO2F 4A3GE 4JK1E 4A3KF 5M3FE 5IYBF 2O5IE 1K83E 1I6VE 3GTOF 3H0GE 1TWHF 4BBSF 5M5YE 1TWFE 1TWGF 1ZYRE 2NVTF 3HOXE 5FLME 3H3VG 4C3JE 3I4MF 2Y0SI 4A3KE 5IYBE 3GTOE 4YFKE 2WB1H 4OINE 3EQLE 1TWHE 3DXJE 1I6HF 4LJZE 4OIPE 1TWGE 2B63E 3S2HF 3I4ME 3PO3F 4QIWH 3GTQF 2R7ZF 4Q5SE 4A3JF 4BY1E 3GTGF 2WAQK 2BE5E 2PMZH 4Y7NF 5M5XF 2O5JE 3CQZE 2CW0E 5C4XF 5M3ME 4XLPE 4OIOE 3GTMF 3GTQE 3HKZK 2R7ZE 5BYHE 4ZH4E 3HOZF 4A3LF 2A69E 4C3IF 3S16F 5M5XE 2KRXA 2JA5F 4C2MF 2NVXF 5C4XE 5TMFE 2JA6F 3S1NF 4A93F 2E2HF 4AYBK 3GTKF 4A3IE 1SFOE 3S1ME 4A3EF 2YU9F 4GZYE 4C3IE 1I3QE 4G7HE 3RZOF 2JA5E 2JA6E 5D4DE 3I4NE 2A6HE 2E2HE 3PO2E 4BBSE 3M3YF 4A3EE 4Y52F 4KMUE 1R9TF 4KN4E 1SMYE 2Y0SH 4YG2E 3HOWF 3RZOE 3GTLF 2NVTE 5FJ8F 2NVYF 3S1RF 5IP9F 1I50F 2R92F 3HOVE 1EIKA 3H3VF 5C3EF 1R9TE 3RZDF 1I6HE 5E17E 3GTJF 5D4CE 3S2DF 3S1RE 1WCMF 4YFNE 5IP9E 3S2HE 4LK0E 1I50E 3PO3E 2R92E 1QKLA 5IP7F 1IW7E 3S14F 5E18E 4A3JE 3GTGE 4LLGE 5M5YF 4A3BF 4Y7NE 4KN7E 1TWAF 4MEXE 5C4JF 3S17F 5IP7E 2R93F 2NVQF 3GTME 2A68E 2WB1I 4BBRF 4G7ZE 3GTPF 1TWCF 4LK1E 3HOZE 3HOUF 4A3LE 4YFXE 1Y1VF 3S16E 3HOVF 1TWAE 2NVXE 4C2ME 3S1NE 5C4JE 3S17E 4C3HF 3FKIF 4A93E 5D4EE 2NVQE 3GTKE 4BBRE 4XSZE 3GTPE 2YU9E 4A3CF 5M5WF 2PPBE 3HOYF 4BY7F 3K7AF 1Y1VE 5C44F 5TMCE 4OIQE 4C3HE 5IYCE 2JA8F 3RZDE 2JA7F 2VUMF 3FKIE 3HKZH 3M3YE 4XSXE 4Y52E 4A3CE 5IYCF 5M5WE 4XLNE 3HOYE 4A3DF 4A3GF 3K7AE 1K83F 3HOWE 4QIWK 3GTLE 5FJ8E 2NVYE 2JA7E 4AYBH 1TWFF 3M4OF 4A3MF 2A6EE
chains in the Genus database with same CATH topology
5C3EE 4A3DE 3GTJE 3S2DE 1WCME 3M4OE 4A3ME 3S14E 1Y1WE 4A3BE 2E2IE 3S1QE 2R93E 4A3FE 2E2JE 1TWCE 3HOUE 2WAQH 5C44E 4BXXE 3S15E 4BY7E 2VUME 2JA8E 1DZFA 4X6AE 5IYDE 4A3GE 5M3FE 1K83E 3H0GE 5M5YE 1TWFE 3HOXE 5FLME 4C3JE 4A3KE 5IYBE 3GTOE 2WB1H 1TWHE 1TWGE 2B63E 3I4ME 4QIWH 4BY1E 2PMZH 3CQZE 5M3ME 3GTQE 2R7ZE 5M5XE 5C4XE 4A3IE 1SFOE 3S1ME 4C3IE 1I3QE 2JA5E 2JA6E 3I4NE 2E2HE 3PO2E 4BBSE 4A3EE 2Y0SH 3RZOE 2NVTE 3HOVE 1EIKA 3H3VF 1R9TE 1I6HE 3S1RE 5IP9E 3S2HE 1I50E 3PO3E 2R92E 4A3JE 3GTGE 4Y7NE 5IP7E 3GTME 3HOZE 4A3LE 3S16E 1TWAE 2NVXE 4C2ME 3S1NE 5C4JE 3S17E 4A93E 2NVQE 3GTKE 4BBRE 3GTPE 2YU9E 1Y1VE 4C3HE 5IYCE 3RZDE 3FKIE 3HKZH 3M3YE 4Y52E 4A3CE 5M5WE 3HOYE 3K7AE 3HOWE 3GTLE 5FJ8E 2NVYE 2JA7E 4AYBH
chains in the Genus database with same CATH homology


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