4X6AF

Crystal structure of yeast rna polymerase ii encountering oxidative cyclopurine dna lesions
Total Genus 17
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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
17
sequence length
84
structure length
84
Chain Sequence
KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
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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/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions.
pubmed doi rcsb
total genus 17
structure length 84
sequence length 84
ec nomenclature
pdb deposition date 2014-12-07

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 4x6aF00
2JA8F 4A3GF 2A69E 4G7OE 2E2IF 3S16F 4BY1F 4YG2E 3WODE 2WAQK 1I50F 3K7AF 4KMUE 4BXXF 1HQME 5IYBF 3S1QF 4C3JF 4A3MF 3I4NF 3GTJF 1TWCF 2B63F 4A3FF 3M4OF 2JA7F 2R93F 4AYBK 4OIOE 1Y1VF 3S1NF 3RZOF 3GTGF 5D4EE 1SMYE 3GTLF 1IW7E 2Y0SI 3GTKF 4C2MF 5E18E 3PO2F 4XLNE 5IP9F 1K83F 5TMFE 5IYCF 3S1MF 3GTQF 3S1RF 4XSXE 2JA5F 5BYHE 2PMZK 5IP7F 4JK1E 1I3QF 4BBRF 5M5WF 5C4JF 3RZDF 3S15F 4OIRE 3M3YF 2WB1I 4LJZE 5M3MF 1YNNK 5M5XF 1ZYRE 5C44F 4YFNE 3S2HF 1TWAF 5D4CE 4BBSF 4MQ9E 3GTPF 3HOWF 5E17E 3GTOF 4LK0E 2R7ZF 1SFOF 1QKLA 5D4DE 4MEXE 1I6HF 2E2JF 3EQLE 5M3FF 4OINE 4OIQE 4A3CF 2A68E 4A3JF 2O5JE 2YU9F 4BY7F 1YNJK 2PPBE 4MEYE 3CQZF 2O5IE 3S17F 4OIPE 4A3LF 5IYDF 3S14F 4Q4ZE 4A93F 4A3BF 4A3IF 2BE5E 3GTMF 4A3EF 4LK1E 3HKZK 5FJ8F 1TWGF 4Q5SE 4KN7E 3DXJE 1TWHF 1Y1WF 4KN4E 3HOXF 2VUMF 5C3EF 5M5YF 5IPLE 5TMCE 3PO3F 4LLGE 1I6VE 2A6HE 4YFXE 3HOUF 1TWFF 4YFKE 2A6EE 4A3DF 4X6AF 4A3KF 3FKIF 2CW0E 4C3HF 4XSZE 4GZYE 4ZH4E 4Y7NF 3H3VG 2JA6F 2NVYF 3HOZF 1R9TF 3HOVF 2NVTF 2R92F 4G7HE 2NVXF 3S2DF 4C3IF 5C4XF 4G7ZE 4XLPE 3I4MF 5FLMF 3H0GF 1WCMF 2NVQF 2E2HF 4Y52F 3HOYF
chains in the Genus database with same CATH superfamily
2JA8F 1TWAE 1I6HE 4A3GF 2A69E 3HOXE 2VUME 4BBSE 5C3EE 4G7OE 3HOWE 2E2IF 3GTOE 2R7ZE 3S16F 4BY1F 4YG2E 3WODE 2WAQK 1I50F 3K7AF 5M3FE 2E2JE 4KMUE 4A3CE 4BXXF 1HQME 3FKIE 5IYBF 4A3JE 2WAQH 3S1QF 4BY7E 4C3JF 4A3MF 3I4NF 3CQZE 3GTJF 1TWCF 2B63F 3H3VF 4A3FF 2JA6E 3S17E 4A3LE 3M4OF 3S14E 2NVXE 4A93E 2JA7F 4A3BE 2R93F 3HOYF 4AYBK 4OIOE 3GTME 1Y1VF 3S1NF 5FJ8E 1TWGE 4QIWK 3RZOF 4AYBH 3H0GE 3GTGF 5D4EE 1SMYE 3GTLF 1IW7E 2Y0SI 1Y1WE 4QIWH 2NVQE 4C2MF 3GTKF 1DZFA 5E18E 5M5YE 3PO2F 4XLNE 3PO3E 2WB1H 5IP9F 1K83F 3HOUE 1TWFE 5TMFE 5IYCF 3S1MF 3GTQF 3S1RF 4XSXE 2JA5F 4A3DE 5BYHE 2PMZK 4X6AE 5IP7F 3K7AE 4A3KE 4JK1E 1I3QF 4BBRF 5M5WF 4C3HE 5C4JF 3RZDF 3S15F 4OIRE 2PMZH 3M3YF 4Y7NE 2WB1I 4LJZE 4C3JE 1YNNK 5M3MF 1ZYRE 5M5XF 5C44F 2NVYE 3HOZE 1R9TE 2Y0SH 3HOVE 4YFNE 2NVTE 1TWAF 3S2HF 2R92E 5D4CE 3S2DE 4BBSF 4MQ9E 3GTPF 4C3IE 3HOWF 5C4XE 5E17E 3GTOF 4LK0E 3I4ME 2R7ZF 1SFOF 1QKLA 5FLME 5D4DE 1WCME 4MEXE 2E2JF 3EQLE 5M3FF 2E2HE 4OINE 4OIQE 2A68E 1I6HF 4A3CF 4Y52E 3HOYE 2JA8E 4A3JF 4A3GE 2O5JE 2YU9F 4BY7F 1YNJK 2PPBE 4MEYE 3CQZF 2O5IE 2E2IE 5IP9E 3S17F 4OIPE 4A3LF 3S16E 5IYDF 4BY1E 3GTQE 3S14F 1I50E 4Q4ZE 4A93F 4A3BF 4BXXE 4A3IF 2BE5E 5IYBE 4A3EF 3GTMF 3S1QE 4LK1E 3HKZK 5FJ8F 1TWGF 4Q5SE 4A3ME 3I4NE 4KN7E 3DXJE 1TWCE 1TWHF 3GTJE 4A3FE 2B63E 3HKZH 3M4OE 1Y1WF 4KN4E 3HOXF 2VUMF 5C3EF 5M5YF 3S2HE 5IPLE 2JA7E 5TMCE 3PO3F 2R93E 4LLGE 1I6VE 3GTPE 2A6HE 4YFXE 1Y1VE 3HOUF 1TWFF 3S1NE 4YFKE 2A6EE 3RZOE 1SFOE 4A3DF 3GTGE 4X6AF 4A3KF 3FKIF 3GTLE 2CW0E 4C3HF 4XSZE 3GTKE 4C2ME 4GZYE 4ZH4E 3PO2E 4Y7NF 2YU9E 3H3VG 2JA6F 1K83E 5IYCE 2NVYF 3HOZF 1R9TF 3S1ME 1EIKA 3HOVF 3S1RE 2NVTF 2R92F 2JA5E 4G7HE 2NVXF 5IYDE 3S2DF 5IP7E 4C3IF 1I3QE 4BBRE 5M5WE 5C4JE 4G7ZE 2KRXA 3RZDE 3S15E 5C4XF 4A3IE 4XLPE 3I4MF 3M3YE 4A3EE 5FLMF 3H0GF 1WCMF 2NVQF 2E2HF 5M5XE 5M3ME 4Y52F 5C44E 1TWHE
chains in the Genus database with same CATH topology
2JA8F 4A3GF 2A69E 4G7OE 2E2IF 3S16F 4BY1F 4YG2E 3WODE 2WAQK 1I50F 3K7AF 4KMUE 4BXXF 1HQME 5IYBF 3S1QF 4C3JF 4A3MF 3I4NF 3GTJF 1TWCF 2B63F 4A3FF 3M4OF 2JA7F 2R93F 4AYBK 4OIOE 1Y1VF 3S1NF 4QIWK 3RZOF 3GTGF 5D4EE 1SMYE 3GTLF 1IW7E 2Y0SI 3GTKF 4C2MF 5E18E 3PO2F 4XLNE 5IP9F 1K83F 5TMFE 5IYCF 3S1MF 3GTQF 3S1RF 4XSXE 2JA5F 5BYHE 2PMZK 5IP7F 4JK1E 1I3QF 4BBRF 5M5WF 5C4JF 3RZDF 3S15F 4OIRE 3M3YF 2WB1I 4LJZE 5M3MF 1YNNK 5M5XF 1ZYRE 5C44F 4YFNE 3S2HF 1TWAF 5D4CE 4BBSF 4MQ9E 3GTPF 3HOWF 5E17E 3GTOF 4LK0E 2R7ZF 1SFOF 1QKLA 5D4DE 4MEXE 1I6HF 2E2JF 3EQLE 5M3FF 4OINE 4OIQE 4A3CF 2A68E 4A3JF 2O5JE 2YU9F 4BY7F 1YNJK 2PPBE 4MEYE 3CQZF 2O5IE 3S17F 4OIPE 4A3LF 5IYDF 3S14F 4Q4ZE 4A93F 4A3BF 4A3IF 2BE5E 3GTMF 4A3EF 4LK1E 3HKZK 5FJ8F 1TWGF 4Q5SE 4KN7E 3DXJE 1TWHF 1Y1WF 4KN4E 3HOXF 2VUMF 5C3EF 5M5YF 5IPLE 5TMCE 3PO3F 4LLGE 1I6VE 2A6HE 4YFXE 3HOUF 1TWFF 4YFKE 2A6EE 4A3DF 4X6AF 4A3KF 3FKIF 2CW0E 4C3HF 4XSZE 4GZYE 4ZH4E 4Y7NF 3H3VG 2JA6F 2NVYF 3HOZF 1R9TF 3HOVF 2NVTF 2R92F 4G7HE 2NVXF 3S2DF 4C3IF 5C4XF 4G7ZE 2KRXA 4XLPE 3I4MF 5FLMF 3H0GF 1WCMF 2NVQF 2E2HF 4Y52F 3HOYF
chains in the Genus database with same CATH homology


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