5C4XF

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
Total Genus 20
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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
20
sequence length
87
structure length
87
Chain Sequence
LKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
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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 20
structure length 87
sequence length 87
ec nomenclature
pdb deposition date 2015-06-18

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 5c4xF00
4BBSF 1ZYRE 5IP7F 4A3JF 5TMFE 5M5WF 4A3FF 4XLPE 4BBRF 1Y1WF 1I6HF 3S2DF 2B63F 5IP9F 3HOWF 3HOYF 5E17E 4G7HE 1WCMF 4AYBK 5D4EE 3HOZF 2WAQK 4A3BF 2Y0SI 2JA5F 1SMYE 1TWCF 5M5XF 4C2MF 4X6AF 2E2HF 4LK1E 4XSZE 1R9TF 2PPBE 3PO2F 2CW0E 3I4MF 4Q5SE 4C3IF 3M4OF 3S17F 3GTMF 3GTGF 4BY1F 4A93F 1TWFF 5IYDF 4A3DF 3H3VG 4LLGE 1IW7E 4KN4E 1QKLA 2R92F 4A3GF 2VUMF 4YG2E 4GZYE 4LJZE 4XSXE 3H0GF 4A3KF 3M3YF 5D4DE 1SFOF 4G7OE 5M3MF 5IYCF 2PMZK 2BE5E 3S1MF 2O5JE 4XLNE 5C44F 3S16F 4KN7E 3S1QF 4OIPE 4C3HF 5E18E 3HOXF 3RZDF 1TWAF 2NVXF 1I3QF 4MEYE 4A3EF 3S1RF 3WODE 4OIQE 3RZOF 1I6VE 5C4XF 1YNNK 2A6HE 3HKZK 4YFKE 3DXJE 4LK0E 4OINE 3CQZF 1I50F 4MQ9E 4OIOE 3GTPF 1Y1VF 4BXXF 4BY7F 3GTJF 5C4JF 3K7AF 4A3LF 3FKIF 4A3IF 3EQLE 5IYBF 5C3EF 2R7ZF 5FJ8F 3GTOF 1YNJK 3S14F 5TMCE 3S15F 4G7ZE 2A6EE 5IPLE 2A68E 1TWHF 3GTQF 4ZH4E 2JA8F 4Y7NF 3S2HF 4OIRE 1HQME 5D4CE 2YU9F 2A69E 3GTLF 3HOVF 1TWGF 3PO3F 4MEXE 2JA6F 4C3JF 3HOUF 5FLMF 2O5IE 2WB1I 2E2JF 4A3CF 4A3MF 4KMUE 5BYHE 2JA7F 5M5YF 4YFXE 4YFNE 2NVTF 3I4NF 4JK1E 3S1NF 2NVQF 2R93F 5M3FF 2E2IF 2NVYF 3GTKF 4Y52F 4Q4ZE 1K83F
chains in the Genus database with same CATH superfamily
4BBSF 1ZYRE 4A3DE 5IP7F 4A3JF 3GTOE 2R93E 1WCME 5TMFE 5M5WF 3S14E 4A3GE 2VUME 4A3FF 2E2IE 2NVYE 4XLPE 4BBRF 1Y1WF 1I6HF 3S2DF 2B63F 5IP9F 3HOWF 3HOYF 4BBSE 5E17E 4G7HE 4A3JE 1SFOE 1TWCE 1WCMF 4AYBK 5D4EE 1DZFA 5M3ME 3HOZF 2YU9E 2WAQK 4A3BF 5C4XF 5IP9E 3HOYE 3HOWE 2Y0SI 5C44E 2JA5F 1SMYE 1TWCF 1TWGE 5M5XF 4C2MF 4C3HE 4X6AF 3HOXE 2E2HF 4LK1E 4XSZE 3M4OE 5FLME 1R9TF 3GTME 2PPBE 3PO2F 4BY1E 4A93E 2JA7E 5M5YE 3I4NE 3S1NE 2CW0E 1I3QE 4C2ME 3I4MF 4A3EE 3S1RE 5M3FE 2E2HE 4Q5SE 4C3IF 3M4OF 3S17F 3GTMF 3GTGF 4BY1F 4A93F 1TWFF 5IYDF 3M3YE 3H3VG 4LLGE 4A3DF 1IW7E 5C4XE 4KN4E 1EIKA 1QKLA 2R92F 3GTPE 2VUMF 2WB1H 4A3GF 5IYCE 4YG2E 4C3IE 4GZYE 4BBRE 1Y1WE 2B63E 4LJZE 4XSXE 3H0GF 4A3KF 1TWFE 3M3YF 2Y0SH 5IYBE 5C3EE 5D4DE 1SFOF 3S16E 4G7OE 5M3MF 5IYCF 2PMZK 4A3BE 2BE5E 3S1MF 2O5JE 4AYBH 3H0GE 4A3KE 4XLNE 5C44F 2JA5E 4KN7E 3S16F 3S1QF 4OIPE 5M5XE 4C3HF 3S2HE 5E18E 3HOXF 4QIWH 3RZDF 1R9TE 1TWAF 2NVXF 3S1QE 1I3QF 1I50E 4MEYE 4A3EF 3S1RF 3HKZH 3GTJE 4BY7E 3WODE 4OIQE 2JA6E 3S17E 3RZOF 3FKIE 1TWAE 1I6VE 3GTGE 1YNNK 2A6HE 2KRXA 3HKZK 5IYDE 3DXJE 4LK0E 4YFKE 2NVXE 4OINE 3CQZF 2R7ZE 1I50F 4MQ9E 4OIOE 2NVTE 1Y1VF 5FJ8E 3GTPF 4BY7F 3GTJF 4BXXF 2R92E 3H3VF 4QIWK 5C4JF 3K7AF 2WAQH 3S15E 3FKIF 4A3LF 4A3IF 4Y52E 3EQLE 5IYBF 5C3EF 3GTQE 2JA8E 3CQZE 2R7ZF 5IP7E 5FJ8F 3GTOF 1YNJK 3S14F 5TMCE 3S1ME 3S15F 4G7ZE 4A3FE 2A6EE 4A3LE 5IPLE 2A68E 4A3IE 1I6HE 3S2DE 1TWHF 3GTLE 3GTQF 4ZH4E 2JA8F 3S1NF 4Y7NF 3S2HF 4OIRE 1HQME 3HOZE 3RZDE 5D4CE 2YU9F 2A69E 1TWHE 3GTLF 3HOVF 2E2JE 4A3CE 4A3ME 4Y7NE 1TWGF 2NVQE 3PO3F 4MEXE 2JA6F 4X6AE 3RZOE 4C3JF 3GTKE 3HOUF 5FLMF 2O5IE 2WB1I 3HOVE 2E2JF 1K83E 4A3CF 3PO2E 4A3MF 4KMUE 5BYHE 2JA7F 5M5YF 4YFXE 1Y1VE 4YFNE 2NVTF 4JK1E 3I4NF 2NVQF 3PO3E 4BXXE 5M5WE 2R93F 3I4ME 5C4JE 3K7AE 2PMZH 5M3FF 2E2IF 2NVYF 4C3JE 3GTKF 3HOUE 4Y52F 4Q4ZE 1K83F
chains in the Genus database with same CATH topology
4BBSF 1ZYRE 5IP7F 4A3JF 5TMFE 5M5WF 4A3FF 4XLPE 4BBRF 1Y1WF 1I6HF 3S2DF 2B63F 5IP9F 3HOWF 3HOYF 5E17E 4G7HE 1WCMF 4AYBK 5D4EE 3HOZF 2WAQK 4A3BF 2Y0SI 2JA5F 1SMYE 1TWCF 5M5XF 4C2MF 4X6AF 2E2HF 4LK1E 4XSZE 1R9TF 2PPBE 3PO2F 2CW0E 3I4MF 4Q5SE 4C3IF 3M4OF 3S17F 3GTMF 3GTGF 4BY1F 4A93F 1TWFF 5IYDF 4A3DF 3H3VG 4LLGE 1IW7E 4KN4E 1QKLA 2R92F 4A3GF 2VUMF 4YG2E 4GZYE 4LJZE 4XSXE 3H0GF 4A3KF 3M3YF 5D4DE 1SFOF 4G7OE 5M3MF 5IYCF 2PMZK 2BE5E 3S1MF 2O5JE 4XLNE 5C44F 3S16F 4KN7E 3S1QF 4OIPE 4C3HF 5E18E 3HOXF 3RZDF 1TWAF 2NVXF 1I3QF 4MEYE 4A3EF 3S1RF 3WODE 4OIQE 3RZOF 1I6VE 5C4XF 1YNNK 2A6HE 2KRXA 3HKZK 4YFKE 3DXJE 4LK0E 4OINE 3CQZF 1I50F 4MQ9E 4OIOE 3GTPF 1Y1VF 4BXXF 4BY7F 3GTJF 4QIWK 5C4JF 3K7AF 4A3LF 3FKIF 4A3IF 3EQLE 5IYBF 5C3EF 2R7ZF 5FJ8F 3GTOF 1YNJK 3S14F 5TMCE 3S15F 4G7ZE 2A6EE 5IPLE 2A68E 1TWHF 3GTQF 4ZH4E 2JA8F 4Y7NF 3S2HF 4OIRE 1HQME 5D4CE 2YU9F 2A69E 3GTLF 3HOVF 1TWGF 3PO3F 4MEXE 2JA6F 4C3JF 3HOUF 5FLMF 2O5IE 2WB1I 2E2JF 4A3CF 4A3MF 4KMUE 5BYHE 2JA7F 5M5YF 4YFXE 4YFNE 2NVTF 3I4NF 4JK1E 3S1NF 2NVQF 2R93F 5M3FF 2E2IF 2NVYF 3GTKF 4Y52F 4Q4ZE 1K83F
chains in the Genus database with same CATH homology


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