3GTJF

Backtracked rna polymerase ii complex with 13mer rna
Total Genus 21
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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
21
sequence length
85
structure length
85
Chain Sequence
EKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
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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
total genus 21
structure length 85
sequence length 85
ec nomenclature
pdb deposition date 2009-03-27

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
F PF01192 RNA_pol_Rpb6 RNA polymerase Rpb6
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit Eukaryotic RPB6 RNA polymerase subunit 3gtjF00
4C3JF 4OINE 1K83F 5D4DE 4C2MF 3S17F 3K7AF 2PPBE 3S2DF 3FKIF 1I50F 1WCMF 1Y1VF 5FJ8F 4BY7F 4BY1F 4A3KF 5TMFE 2WAQK 4LJZE 3HOVF 2R92F 4LLGE 4JK1E 5D4CE 2A68E 3RZOF 4OIRE 3HOUF 4OIOE 4A93F 5M5WF 1QKLA 4A3GF 4OIQE 2B63F 4MQ9E 3GTJF 4KMUE 2A69E 4Q4ZE 5FLMF 2JA7F 3HOWF 4A3BF 4KN7E 2VUMF 2E2IF 3S2HF 4YFXE 3PO2F 3RZDF 4A3CF 3GTQF 3HKZK 3S1MF 5BYHE 3DXJE 4G7ZE 2YU9F 2JA6F 5E17E 2Y0SI 2NVYF 3WODE 4BBSF 1ZYRE 2JA5F 3S15F 4A3JF 5M5XF 4AYBK 1R9TF 2O5JE 4MEXE 4XSXE 5C4JF 3S1QF 3S1RF 1I6HF 1TWGF 2A6EE 3GTOF 3S16F 1TWFF 5IYDF 2JA8F 2CW0E 4BXXF 4C3HF 4Y7NF 5M3FF 1TWAF 4Y52F 4G7HE 3I4MF 2WB1I 2E2HF 3GTMF 4BBRF 5IPLE 1SMYE 5C44F 4XSZE 4OIPE 2E2JF 4G7OE 4A3EF 5E18E 5C4XF 4YFNE 5D4EE 5C3EF 3M4OF 2O5IE 3H0GF 4YG2E 3HOXF 1HQME 5IP7F 5IYCF 5M3MF 4XLNE 4A3MF 3CQZF 4ZH4E 5IP9F 3GTPF 3S1NF 5M5YF 3GTLF 3PO3F 3GTKF 3M3YF 4A3LF 3GTGF 4LK0E 1TWHF 1I6VE 4X6AF 2NVXF 4LK1E 3HOYF 1I3QF 3EQLE 1SFOF 3I4NF 4YFKE 2BE5E 1Y1WF 1YNJK 4XLPE 1YNNK 4A3IF 2R93F 2NVTF 2A6HE 4A3FF 2NVQF 4Q5SE 4C3IF 3HOZF 4MEYE 4GZYE 2R7ZF 2PMZK 3H3VG 5IYBF 5TMCE 4A3DF 1TWCF 3S14F 4KN4E 1IW7E
chains in the Genus database with same CATH superfamily
4C3JF 1SFOE 4OINE 1K83F 3I4NE 2WAQH 1Y1WE 5D4DE 4C2MF 2E2HE 3S17F 3K7AF 4BBRE 4A3IE 2PPBE 2R93E 2NVTE 3S2DF 3FKIF 1I50F 1WCMF 1Y1VF 2E2JE 4C3IE 5FJ8F 4GZYE 3M4OE 4BY7F 4BY1F 4A3KF 5TMFE 2WAQK 4LJZE 3HOVF 3S14E 2R92F 4LLGE 4JK1E 1K83E 3GTPE 5D4CE 2A68E 4C2ME 3RZOF 3S17E 3K7AE 4Y7NE 4OIRE 4OIOE 3HOUF 4A93F 3FKIE 1I50E 5M5WF 2NVXE 3HOYE 1Y1VE 5FJ8E 1QKLA 4A3GF 4OIQE 2B63F 4MQ9E 3HKZH 4A3KE 4BY1E 3GTJF 2KRXA 4KMUE 3HOVE 2A69E 4Q4ZE 5FLMF 2R92E 2JA7F 3HOWF 4A3FE 4KN7E 2NVQE 2VUMF 4A3BF 2E2IF 3S2HF 3H3VF 3HOZE 4YFXE 3RZOE 3PO2F 4AYBH 2R7ZE 3HOUE 3RZDF 4A3CF 3GTQF 3HKZK 5IYBE 5BYHE 3S1MF 3DXJE 4A3DE 1TWCE 5M5WE 4G7ZE 2YU9F 2JA6F 5E17E 2Y0SI 2B63E 2NVYF 4C3JE 3WODE 4BBSF 1ZYRE 3GTJE 2JA5F 3S15F 4A3JF 5M5XF 4AYBK 1R9TF 2O5JE 4MEXE 3S2DE 4XSXE 1WCME 5C4JF 2JA7E 3HOWE 3S1QF 4A3BE 3S1RF 1I6HF 1TWGF 2A6EE 2VUME 3GTOF 1TWFF 3S16F 5IYDF 2JA8F 2CW0E 4BXXF 4C3HF 3RZDE 3GTQE 3S1ME 4BY7E 1DZFA 4Y7NF 5M3FF 2YU9E 2JA6E 1TWAF 4Y52F 4G7HE 3I4MF 2WB1I 2E2HF 3GTMF 4BBRF 3S15E 2JA5E 5IPLE 1SMYE 4A3JE 5M5XE 5C44F 4XSZE 4A93E 5C4XF 4OIPE 5C4JE 2E2JF 3S1QE 4A3EF 4G7OE 5E18E 3S1RE 4YFNE 3S16E 5D4EE 5C3EF 1TWFE 3M4OF 2O5IE 5IYDE 4A3GE 2JA8E 3H0GF 4YG2E 3HOXF 1HQME 5IP7F 5IYCF 2WB1H 5M3MF 4XLNE 4QIWH 5M3FE 4A3MF 5FLME 3CQZF 4ZH4E 5IP9F 3GTPF 1TWAE 3S1NF 4Y52E 5M5YF 3I4ME 3GTLF 2E2IE 3GTME 3PO3F 3GTKF 3M3YF 3S2HE 4A3LF 3GTGF 3PO2E 4LK0E 5C44E 1TWHF 1I6VE 4A3CE 2Y0SH 2NVXF 4LK1E 3HOYF 4X6AF 1I3QF 3EQLE 4A3EE 5C4XE 2PMZH 4QIWK 5C3EE 1SFOF 3I4NF 4YFKE 2BE5E 3H0GE 2NVYE 3HOXE 1Y1WF 4BBSE 1EIKA 1YNJK 4XLPE 5IP7E 1YNNK 5IYCE 4A3IF 2R93F 5M3ME 2NVTF 2A6HE 4A3ME 1R9TE 3CQZE 4A3FF 2NVQF 4Q5SE 5IP9E 4C3IF 3S1NE 3HOZF 5M5YE 4MEYE 1I6HE 3GTLE 1TWGE 3GTOE 2R7ZF 2PMZK 3GTKE 3H3VG 3M3YE 5IYBF 5TMCE 3PO3E 3GTGE 4A3LE 4BXXE 1TWCF 1TWHE 4C3HE 3S14F 4A3DF 4X6AE 4KN4E 1IW7E 1I3QE
chains in the Genus database with same CATH topology
4C3JF 4OINE 1K83F 5D4DE 4C2MF 3S17F 3K7AF 2PPBE 3S2DF 3FKIF 1I50F 1WCMF 1Y1VF 5FJ8F 4BY7F 4BY1F 4A3KF 5TMFE 2WAQK 4LJZE 3HOVF 2R92F 4LLGE 4JK1E 5D4CE 2A68E 3RZOF 4OIRE 3HOUF 4OIOE 4A93F 5M5WF 1QKLA 4A3GF 4OIQE 2B63F 4MQ9E 3GTJF 2KRXA 4KMUE 2A69E 4Q4ZE 5FLMF 2JA7F 3HOWF 4A3BF 4KN7E 2VUMF 2E2IF 3S2HF 4YFXE 3PO2F 3RZDF 4A3CF 3GTQF 3HKZK 3S1MF 5BYHE 3DXJE 4G7ZE 2YU9F 2JA6F 5E17E 2Y0SI 2NVYF 3WODE 4BBSF 1ZYRE 2JA5F 3S15F 4A3JF 5M5XF 4AYBK 1R9TF 2O5JE 4MEXE 4XSXE 5C4JF 3S1QF 3S1RF 1I6HF 1TWGF 2A6EE 3GTOF 3S16F 1TWFF 5IYDF 2JA8F 2CW0E 4BXXF 4C3HF 4Y7NF 5M3FF 1TWAF 4Y52F 4G7HE 3I4MF 2WB1I 2E2HF 3GTMF 4BBRF 5IPLE 1SMYE 5C44F 4XSZE 4OIPE 2E2JF 4G7OE 4A3EF 5E18E 5C4XF 4YFNE 5D4EE 5C3EF 3M4OF 2O5IE 3H0GF 4YG2E 3HOXF 1HQME 5IP7F 5IYCF 5M3MF 4XLNE 4A3MF 3CQZF 4ZH4E 5IP9F 3GTPF 3S1NF 5M5YF 3GTLF 3PO3F 3GTKF 3M3YF 4A3LF 3GTGF 4LK0E 1TWHF 1I6VE 4X6AF 2NVXF 4LK1E 3HOYF 1I3QF 3EQLE 4QIWK 1SFOF 3I4NF 4YFKE 2BE5E 1Y1WF 1YNJK 4XLPE 1YNNK 4A3IF 2R93F 2NVTF 2A6HE 4A3FF 2NVQF 4Q5SE 4C3IF 3HOZF 4MEYE 4GZYE 2R7ZF 2PMZK 3H3VG 5IYBF 5TMCE 4A3DF 1TWCF 3S14F 4KN4E 1IW7E
chains in the Genus database with same CATH homology


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