3GTME

Co-complex of backtracked rna polymerase ii with tfiis
Total Genus 45
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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
45
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, transferase/dna-rna hybrid
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
pubmed doi rcsb
source organism Saccharomyces cerevisiae
total genus 45
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2009-03-27

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 3gtmE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 3gtmE02
3FKIE 3S1RE 1TWGE 1TWHE 4A93E 1WCME 2PMZH 2NVTE 4A3DE 3S15E 1DZFA 3I4NE 3RZDE 4A3BE 4A3EE 3S1ME 4A3LE 3HOVE 3M4OE 2R93E 3GTQE 5IYCE 2JA5E 3GTME 3GTLE 4BXXE 3H3VF 4BBRE 3HOZE 4A3ME 2YU9E 4BY7E 2B63E 5FJ8E 2JA6E 3GTKE 3PO2E 4AYBH 3S17E 4C2ME 3S14E 4A3FE 3S1QE 3GTOE 2NVQE 3M3YE 3RZOE 4X6AE 4BY1E 2E2IE 4A3IE 3S2HE 3S1NE 4QIWH 3GTJE 5IYBE 1Y1WE 3S16E 1TWCE 5M5YE 2R92E 2WAQH 1I50E 2VUME 5FLME 4A3GE 2R7ZE 3GTPE 3HOWE 1K83E 4Y7NE 4A3JE 4C3JE 5M5WE 3HOUE 5C4XE 1R9TE 1SFOE 2JA8E 5C44E 2E2JE 5IYDE 5C3EE 2Y0SH 3K7AE 1Y1VE 5M3ME 5IP7E 4A3KE 4Y52E 3PO3E 3HOYE 4C3IE 4A3CE 1TWAE 2NVXE 3CQZE 2JA7E 4BBSE 5M3FE 3HKZH 4C3HE 3GTGE 3S2DE 2NVYE 2WB1H 1EIKA 5C4JE 3H0GE 5IP9E 3HOXE 2E2HE 3I4ME 1I6HE 1I3QE 5M5XE 1TWFE
chains in the Genus database with same CATH superfamily
3HOWF 3FKIE 1K83F 4Y7NF 4A3JF 3S1RE 1TWGE 1TWHE 5TMFE 4C3JF 5M5WF 3HOUF 4GZYE 5C4XF 1R9TF 4MEYE 4A93E 1YNNK 1SFOF 1WCME 2PMZH 5C44F 2PPBE 2JA8F 4YFNE 2E2JF 2NVTE 5IYDF 4BY1F 3K7AF 4A3DE 2KRXA 1Y1VF 3S15E 3S1NF 5M3MF 5D4CE 1DZFA 3I4NE 3RZDE 4A3BE 1I6VE 1SMYE 5IP7F 4A3EE 3S1ME 4A3LE 3HOVE 3M4OE 4LJZE 4Y52F 3PO3F 2R93E 4C3IF 4YFKE 2O5JE 3GTQE 4A3CF 1TWAF 5IYCE 2JA5E 3GTME 3GTLE 4BXXE 3H3VF 1QKLA 2NVXF 1HQME 5FLMF 2JA7F 2R7ZF 4BBSF 4BBRE 3HOZE 5M3FF 5E17E 4A3ME 2YU9E 2A69E 4MQ9E 4BY7E 2PMZK 2B63E 4XSZE 4C3HF 5FJ8E 4AYBK 4OIOE 3GTGF 2NVYF 2JA6E 3GTKE 3PO2E 5C4JF 4AYBH 3S17E 3H0GF 5IP9F 5BYHE 5C3EF 3HOXF 2E2HF 4YG2E 1I3QF 1I6HF 3I4MF 4C2ME 5M5XF 3S14E 3S1MF 4A3FE 1TWFF 3DXJE 3S1QE 3GTOE 3FKIF 2NVQE 3M3YE 3RZOE 4OIQE 4X6AE 4BY1E 2E2IE 4ZH4E 3S1RF 1TWGF 3WODE 1TWHF 4A3IE 3S2HE 4A3KF 3S1NE 3HOYF 1IW7E 4JK1E 4QIWH 3GTJE 4A93F 1WCMF 5IYBE 5D4EE 4X6AF 2WAQK 1Y1WE 5TMCE 3S16E 4KN4E 2NVTF 3CQZF 5E18E 1TWCE 5M5YE 3EQLE 4A3DF 2R92E 3S15F 2WAQH 1I50E 1YNJK 3I4NF 3RZDF 4A3BF 4A3EF 4A3LF 4YFXE 2VUME 3HOVF 3M4OF 5FLME 4A3GE 2R7ZE 3GTPE 3S2DF 3HOWE 2R93F 1K83E 4Y7NE 4A3JE 3GTQF 4C3JE 5M5WE 3HOUE 4Q5SE 2JA5F 5C4XE 3GTLF 2CW0E 1R9TE 3GTMF 4BXXF 1SFOE 2JA8E 5C44E 4BBRF 4Q4ZE 2E2JE 3HOZF 5IYDE 2Y0SI 4QIWK 4A3MF 2YU9F 5C3EE 4BY7F 2Y0SH 3K7AE 1Y1VE 2B63F 5M3ME 5FJ8F 2A68E 1ZYRE 2O5IE 4LK1E 5IP7E 4G7OE 2JA6F 2A6HE 3GTKF 3PO2F 3S17F 4A3KE 4Y52E 3PO3E 4OINE 3HOYE 4C2MF 4LLGE 3S14F 4A3FF 4C3IE 2A6EE 4G7HE 3S1QF 3GTOF 4A3CE 1TWAE 4XSXE 2NVXE 3CQZE 2JA7E 4BBSE 3HKZK 2E2IF 4OIRE 2NVQF 3M3YF 3RZOF 4A3IF 3S2HF 5M3FE 4XLPE 3HKZH 3GTJF 5IYBF 4C3HE 2BE5E 4LK0E 1Y1WF 3S16F 5IYCF 4MEXE 1TWCF 5M5YF 2WB1I 4OIPE 4KMUE 3GTGE 3S2DE 2NVYE 2WB1H 4G7ZE 2R92F 1EIKA 1I50F 5C4JE 3H3VG 3H0GE 5IP9E 3HOXE 2E2HE 3I4ME 1I6HE 4XLNE 1I3QE 4KN7E 5D4DE 5M5XE 2VUMF 5IPLE 4A3GF 1TWFE 3GTPF
chains in the Genus database with same CATH topology
3FKIE 3S1RE 1TWGE 1TWHE 4A93E 1WCME 2PMZH 2NVTE 4A3DE 3S15E 1DZFA 3I4NE 3RZDE 4A3BE 4A3EE 3S1ME 4A3LE 3HOVE 3M4OE 2R93E 3GTQE 5IYCE 2JA5E 3GTME 3GTLE 4BXXE 3H3VF 4BBRE 3HOZE 4A3ME 2YU9E 4BY7E 2B63E 5FJ8E 2JA6E 3GTKE 3PO2E 4AYBH 3S17E 4C2ME 3S14E 4A3FE 3S1QE 3GTOE 2NVQE 3M3YE 3RZOE 4X6AE 4BY1E 2E2IE 4A3IE 3S2HE 3S1NE 4QIWH 3GTJE 5IYBE 1Y1WE 3S16E 1TWCE 5M5YE 2R92E 2WAQH 1I50E 2VUME 5FLME 4A3GE 2R7ZE 3GTPE 3HOWE 1K83E 4Y7NE 4A3JE 4C3JE 5M5WE 3HOUE 5C4XE 1R9TE 1SFOE 2JA8E 5C44E 2E2JE 5IYDE 5C3EE 2Y0SH 3K7AE 1Y1VE 5M3ME 5IP7E 4A3KE 4Y52E 3PO3E 3HOYE 4C3IE 4A3CE 1TWAE 2NVXE 3CQZE 2JA7E 4BBSE 5M3FE 3HKZH 4C3HE 3GTGE 3S2DE 2NVYE 2WB1H 1EIKA 5C4JE 3H0GE 5IP9E 3HOXE 2E2HE 3I4ME 1I6HE 1I3QE 5M5XE 1TWFE
chains in the Genus database with same CATH homology


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