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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molecule tags Transferase/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
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)
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
4LK1E 4BY1F 2B63F 3S14F 3HOXF 3S1NF 1TWHF 2E2JF 1TWFF 4YFKE 5C3EF 4JK1E 2NVYF 5D4DE 4C2MF 2R92F 2A69E 4MQ9E 1I6VE 4C3IF 2E2HF 3GTPF 3HOWF 1WCMF 3M4OF 3HOYF 3S2DF 5M5WF 5C4JF 5BYHE 4MEYE 4C3HF 2PMZK 5C44F 4A93F 4GZYE 4X6AF 1I6HF 3S1MF 5E18E 3GTLF 2NVQF 2JA8F 4Q5SE 5M3MF 5IYCF 2O5IE 4XSZE 3K7AF 5IPLE 4A3GF 3DXJE 3GTKF 5TMCE 5E17E 1Y1WF 1YNNK 4LLGE 1HQME 1IW7E 4A3MF 3H3VG 4C3JF 2A68E 3HOZF 1I3QF 4A3CF 3GTGF 4BBRF 4KN7E 4OINE 4KMUE 4XLNE 1Y1VF 4XLPE 3HOUF 5IP7F 1K83F 4A3FF 1QKLA 4Q4ZE 1TWGF 4OIPE 2O5JE 3S15F 4LJZE 5IP9F 4G7ZE 4A3KF 2WAQK 5M3FF 2CW0E 4Y7NF 4G7OE 2PPBE 4YFNE 2VUMF 4A3EF 4A3DF 2JA5F 4XSXE 3S1QF 4A3BF 1TWAF 4BXXF 2Y0SI 4KN4E 3RZOF 3S2HF 2JA6F 4OIOE 3FKIF 5IYDF 3EQLE 3GTMF 3I4MF 3GTQF 2R93F 1I50F 4AYBK 3WODE 2A6EE 5D4EE 2NVXF 4A3JF 3S17F 5C4XF 1TWCF 5IYBF 5FJ8F 5M5YF 4BY7F 3HKZK 2R7ZF 2NVTF 3PO3F 3CQZF 3GTOF 4BBSF 3I4NF 5FLMF 4A3LF 2A6HE 3S16F 4ZH4E 4YFXE 3S1RF 3H0GF 2E2IF 4A3IF 1SFOF 3M3YF 3GTJF 4Y52F 3PO2F 3HOVF 1YNJK 4MEXE 1SMYE 2BE5E 1ZYRE 4YG2E 2WB1I 5M5XF 4OIRE 4LK0E 5D4CE 3RZDF 4OIQE 4G7HE 2JA7F 2YU9F 5TMFE 1R9TF
chains in the Genus database with same CATH superfamily
4A3BE 4LK1E 1TWAE 4BY1F 3GTKE 4BXXE 2B63F 3S14F 3S2HE 3HOXF 3S1NF 1TWHF 2E2JF 1TWFF 4YFKE 5C3EF 4JK1E 3FKIE 4X6AF 2NVYF 5D4DE 4C2MF 2R92F 2A69E 4MQ9E 1I6VE 5IYDE 4AYBH 1I3QE 4C3IF 2E2HF 3GTME 3GTQE 3GTPF 3HOWF 3I4ME 3HOZE 4BBRE 1WCMF 3M4OF 3HOYF 3S2DF 5M5WF 2NVXE 5IP7E 5C4JF 1DZFA 3HKZH 1TWGE 5C4XE 5BYHE 4MEYE 2PMZK 1TWCE 4C3HF 5C44F 5IYBE 5FJ8E 1I6HF 5M5YE 3S15E 5E18E 3GTLF 3S1MF 2NVQF 2NVTE 4BY7E 2JA8F 4A93F 4Q5SE 5M3MF 5IYCF 3GTOE 4BBSE 2O5IE 4XSZE 3K7AF 3I4NE 5FLME 5IPLE 4A3GF 4A3EE 3S16E 3S1QE 3DXJE 4QIWK 3GTKF 5TMCE 3RZOE 4A3IE 2JA6E 1SFOE 5E17E 3M3YE 1Y1WF 1YNNK 4LLGE 1IW7E 1HQME 4A3MF 3GTJE 3H3VG 4Y52E 3PO2E 3HOVE 4C3JF 2A68E 3HOZF 1I3QF 4A3CF 2R93E 1I50E 3GTGF 4BBRF 4KN7E 4OINE 4KMUE 4XLNE 1Y1VF 4A3JE 3RZDE 4XLPE 3HOUF 1K83F 5IP7F 4A3FF 1QKLA 2JA7E 3S17E 4Q4ZE 2YU9E 1TWGF 3GTGE 4OIPE 2O5JE 3S15F 2R7ZE 3PO3E 4LJZE 5IP9F 4G7ZE 4BY1E 2B63E 3CQZE 3S14E 4A3KF 2WAQK 1TWHE 5M3FF 2E2JE 2CW0E 4Y7NF 4A3LE 2PPBE 4G7OE 2NVYE 4YFNE 2VUMF 4A3EF 4A3DF 2JA5F 4XSXE 3S1RE 2E2HE 3S1QF 4A3BF 3H0GE 1TWAF 4BXXF 2E2IE 3HOWE 2Y0SI 4KN4E 3RZOF 3S2HF 2Y0SH 1WCME 2JA6F 2PMZH 5M5WE 4OIOE 3FKIF 5IYDF 3EQLE 5C44E 3GTMF 2KRXA 4A93E 3I4MF 4X6AE 3GTQF 1I6HE 2R93F 3GTLE 1I50F 5M5XE 4AYBK 5IYCE 3WODE 2A6EE 5D4EE 2NVXF 4A3JF 3S17F 4QIWH 4A3GE 5C4XF 1TWCF 1R9TE 5IYBF 5FJ8F 5M5YF 4BY7F 3HKZK 2R7ZF 2NVTF 3PO3F 3HOXE 3CQZF 3S1NE 3GTOF 4BBSF 1TWFE 5C3EE 1EIKA 1Y1WE 3I4NF 5FLMF 4A3LF 4A3ME 4C2ME 2A6HE 3S16F 4ZH4E 4C3IE 2R92E 4YFXE 3H3VF 4C3JE 3S1RF 3GTPE 4A3CE 3H0GF 2E2IF 4A3IF 3M4OE 3HOYE 3S2DE 1SFOF 3M3YF 1Y1VE 5C4JE 3HOUE 1K83E 3GTJF 4Y52F 4A3FE 4C3HE 3PO2F 3HOVF 3S1ME 1YNJK 4MEXE 1SMYE 2WAQH 2BE5E 5IP9E 1ZYRE 2JA8E 2NVQE 4YG2E 5M3ME 2WB1I 5M5XF 4OIRE 2WB1H 4LK0E 5D4CE 3K7AE 4A3KE 5M3FE 3RZDF 4GZYE 4Y7NE 4OIQE 4G7HE 2JA7F 2YU9F 2VUME 4A3DE 2JA5E 5TMFE 1R9TF
chains in the Genus database with same CATH topology
4LK1E 4BY1F 2B63F 3S14F 3HOXF 3S1NF 1TWHF 2E2JF 1TWFF 4YFKE 5C3EF 4JK1E 2NVYF 5D4DE 4C2MF 2R92F 2A69E 4MQ9E 1I6VE 4C3IF 2E2HF 3GTPF 3HOWF 1WCMF 3M4OF 3HOYF 3S2DF 5M5WF 5C4JF 5BYHE 4MEYE 4C3HF 2PMZK 5C44F 4A93F 4GZYE 4X6AF 1I6HF 3S1MF 5E18E 3GTLF 2NVQF 2JA8F 4Q5SE 5M3MF 5IYCF 2O5IE 4XSZE 3K7AF 5IPLE 4A3GF 3DXJE 4QIWK 3GTKF 5TMCE 5E17E 1Y1WF 1YNNK 4LLGE 1HQME 1IW7E 4A3MF 3H3VG 4C3JF 2A68E 3HOZF 1I3QF 4A3CF 3GTGF 4BBRF 4KN7E 4OINE 4KMUE 4XLNE 1Y1VF 4XLPE 3HOUF 5IP7F 1K83F 4A3FF 1QKLA 4Q4ZE 1TWGF 4OIPE 2O5JE 3S15F 4LJZE 5IP9F 4G7ZE 4A3KF 2WAQK 5M3FF 2CW0E 4Y7NF 4G7OE 2PPBE 4YFNE 2VUMF 4A3EF 4A3DF 2JA5F 4XSXE 3S1QF 4A3BF 1TWAF 4BXXF 2Y0SI 4KN4E 3RZOF 3S2HF 2JA6F 4OIOE 3FKIF 5IYDF 3EQLE 3GTMF 2KRXA 3I4MF 3GTQF 2R93F 1I50F 4AYBK 3WODE 2A6EE 5D4EE 2NVXF 4A3JF 3S17F 5C4XF 1TWCF 5IYBF 5FJ8F 5M5YF 4BY7F 3HKZK 2R7ZF 2NVTF 3PO3F 3CQZF 3GTOF 4BBSF 3I4NF 5FLMF 4A3LF 2A6HE 3S16F 4ZH4E 4YFXE 3S1RF 3H0GF 2E2IF 4A3IF 1SFOF 3M3YF 3GTJF 4Y52F 3PO2F 3HOVF 1YNJK 4MEXE 1SMYE 2BE5E 1ZYRE 4YG2E 2WB1I 5M5XF 4OIRE 4LK0E 5D4CE 3RZDF 4OIQE 4G7HE 2JA7F 2YU9F 5TMFE 1R9TF
chains in the Genus database with same CATH homology


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