2NVQE

Rna polymerase ii elongation complex in 150 mm mg+2 with 2'dutp
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,transferase/dna-rna hybrid
molecule keywords 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'
publication title Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
pubmed doi rcsb
total genus 59
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2006-11-13

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 2nvqE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 2nvqE02
3S14E 3GTKE 4BXXE 5M3ME 3GTPE 3M4OE 5FLME 3S2DE 4A3IE 2WAQH 3S2HE 1TWAE 4Y7NE 4A3CE 2E2HE 2E2IE 4QIWH 5IP7E 3HOZE 1I50E 3S16E 1I6HE 1EIKA 5IYBE 2R7ZE 2NVQE 1DZFA 4C3HE 2WB1H 5M5WE 3HOVE 2R93E 3M3YE 3S15E 3HOXE 4A3ME 3RZDE 3GTME 3HOWE 3GTGE 2NVXE 3HOUE 4A3KE 3H0GE 1I3QE 3PO3E 3HKZH 3S1QE 5M5XE 2NVTE 3S1RE 2PMZH 2JA6E 2JA8E 3GTQE 3S1ME 5M5YE 1SFOE 4A93E 4A3GE 1TWHE 3H3VF 4BY7E 3GTOE 3GTLE 4A3DE 5C3EE 4BBRE 2VUME 2Y0SH 3I4NE 3I4ME 1TWFE 4BBSE 4A3JE 1R9TE 4A3EE 1TWCE 4C3IE 5IYCE 3HOYE 2R92E 3RZOE 1Y1VE 2JA7E 4C3JE 4A3FE 3S17E 2B63E 4C2ME 3PO2E 5IYDE 5C4XE 4A3BE 2YU9E 3FKIE 3CQZE 3GTJE 3S1NE 1WCME 5C4JE 5IP9E 4A3LE 2NVYE 2E2JE 2JA5E 5C44E 4BY1E 1K83E 4Y52E 5FJ8E 1Y1WE 5M3FE 4AYBH 3K7AE 4X6AE 1TWGE
chains in the Genus database with same CATH superfamily
5IYBF 4A3GF 4KMUE 3S14E 3GTKE 4BXXE 5M3ME 3GTPE 4MEXE 3M4OE 3DXJE 5FLME 3S2DE 4A3IE 2WAQH 3HOVF 5C3EF 2R93F 3S2HE 4BBRF 1TWAE 5IPLE 4Y7NE 4A3CE 4G7OE 2E2HE 2E2IE 4QIWH 3I4NF 3M3YF 5IP7E 3HOZE 1I50E 3S16E 3HOXF 3GTMF 3I4MF 1I6HE 3HOWF 1EIKA 5IYBE 3GTGF 5E18E 2NVXF 3HOUF 4A3KF 2O5JE 1I3QF 3PO3F 4LK1E 3S1QF 4KN4E 2R7ZE 5M5XF 2NVQE 1DZFA 4Q4ZE 2NVTF 4OIPE 5IYCF 3S1RF 3RZOF 4C3HE 2WB1H 2JA6F 3GTQF 3S1MF 5M5WE 5M5YF 3HOVE 2R93E 5D4EE 4A3FF 2WB1I 1SFOF 3M3YE 3S15E 4G7ZE 3S17F 4A93F 4XSZE 3HOXE 4A3ME 3RZDE 3GTME 3HOWE 1TWHF 2KRXA 3GTGE 2NVXE 4JK1E 3HOUE 4A3KE 3H0GE 4BY7F 1I3QE 3PO3E 3HKZH 3S1QE 4XLNE 4MQ9E 5M5XE 2NVTE 3GTLF 3GTOF 4A3DF 3S1RE 2PMZH 2JA6E 2JA8E 3GTQE 3S1ME 4OIRE 5M5YE 2A68E 4A3BF 2VUMF 1YNJK 5TMFE 1SFOE 1TWFF 4BBSF 4A93E 3GTJF 4LJZE 4A3JF 4A3GE 1TWHE 4ZH4E 4MEYE 4YFKE 4GZYE 1R9TF 4A3EF 3WODE 3H3VF 4BY7E 1QKLA 1TWCF 4C3IF 3GTOE 3GTLE 2R92F 3HOYF 4A3DE 5D4DE 5E17E 1Y1VF 4XSXE 4A3LF 5C3EE 1YNNK 2JA5F 4BBRE 5C44F 4C3JF 2JA7F 2VUME 2Y0SH 4KN7E 3I4NE 3S15F 2B63F 3I4ME 5FJ8F 1TWFE 4BBSE 4LK0E 4A3JE 4AYBK 2Y0SI 4C2MF 1R9TE 4A3EE 3PO2F 1TWCE 4C3IE 2BE5E 5IYDF 5IYCE 3HOYE 2R92E 3RZOE 5C4XF 3GTKF 1Y1VE 2YU9F 2JA7E 4C3JE 3M4OF 4A3FE 3FKIF 5FLMF 3S17E 5BYHE 2WAQK 2PMZK 2B63E 4YG2E 3CQZF 3H3VG 3S1NF 1WCMF 4XLPE 4C2ME 2A69E 4QIWK 3PO2E 5C4JF 2E2HF 5IP9F 1I50F 4OIQE 5IYDE 1IW7E 5C4XE 2NVYF 2E2JF 4LLGE 4A3BE 2YU9E 2CW0E 4BY1F 1K83F 4Y52F 2NVQF 3FKIE 2R7ZF 4OINE 2O5IE 4C3HF 3CQZE 3GTJE 1Y1WF 5M5WF 3S1NE 1I6VE 1WCME 1ZYRE 5M3FF 3K7AF 3EQLE 5D4CE 5C4JE 5TMCE 4X6AF 5IP9E 1HQME 1SMYE 1TWGF 4A3MF 3RZDF 3S14F 4BXXF 3HKZK 4A3LE 5M3MF 4G7HE 2NVYE 2E2JE 3H0GF 2JA5E 5C44E 3GTPF 4YFXE 4BY1E 1K83E 4Y52E 2PPBE 4YFNE 3S2DF 5FJ8E 2A6EE 4A3IF 1Y1WE 2JA8F 5M3FE 3S2HF 1TWAF 4OIOE 4Y7NF 4A3CF 4AYBH 2E2IF 3K7AE 4X6AE 2A6HE 5IP7F 3HOZF 3S16F 4Q5SE 1I6HF 1TWGE
chains in the Genus database with same CATH topology
3S14E 3GTKE 4BXXE 5M3ME 3GTPE 3M4OE 5FLME 3S2DE 4A3IE 2WAQH 3S2HE 1TWAE 4Y7NE 4A3CE 2E2HE 2E2IE 4QIWH 5IP7E 3HOZE 1I50E 3S16E 1I6HE 1EIKA 5IYBE 2R7ZE 2NVQE 1DZFA 4C3HE 2WB1H 5M5WE 3HOVE 2R93E 3M3YE 3S15E 3HOXE 4A3ME 3RZDE 3GTME 3HOWE 3GTGE 2NVXE 3HOUE 4A3KE 3H0GE 1I3QE 3PO3E 3HKZH 3S1QE 5M5XE 2NVTE 3S1RE 2PMZH 2JA6E 2JA8E 3GTQE 3S1ME 5M5YE 1SFOE 4A93E 4A3GE 1TWHE 3H3VF 4BY7E 3GTOE 3GTLE 4A3DE 5C3EE 4BBRE 2VUME 2Y0SH 3I4NE 3I4ME 1TWFE 4BBSE 4A3JE 1R9TE 4A3EE 1TWCE 4C3IE 5IYCE 3HOYE 2R92E 3RZOE 1Y1VE 2JA7E 4C3JE 4A3FE 3S17E 2B63E 4C2ME 3PO2E 5IYDE 5C4XE 4A3BE 2YU9E 3FKIE 3CQZE 3GTJE 3S1NE 1WCME 5C4JE 5IP9E 4A3LE 2NVYE 2E2JE 2JA5E 5C44E 4BY1E 1K83E 4Y52E 5FJ8E 1Y1WE 5M3FE 4AYBH 3K7AE 4X6AE 1TWGE
chains in the Genus database with same CATH homology


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