3S1RF

Rna polymerase ii initiation complex with a 5-nt 3'-deoxy rna soaked with gtp
Total Genus 24
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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
24
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/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Initiation complex structure and promoter proofreading.
pubmed doi rcsb
total genus 24
structure length 85
sequence length 85
ec nomenclature
pdb deposition date 2011-05-16

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 3s1rF00
1SMYE 5E17E 1IW7E 3HKZK 5IYDF 2E2HF 4A93F 5D4DE 4OIRE 3RZDF 3K7AF 3M3YF 2BE5E 4A3CF 4A3IF 5M3FF 3DXJE 4ZH4E 4Y7NF 5TMFE 4BBSF 3S16F 5D4EE 1TWAF 4Y52F 4A3DF 3PO2F 2E2IF 5IYCF 2PMZK 4LK1E 3M4OF 4BY7F 3HOXF 3HOYF 4G7OE 2R92F 4MEXE 2PPBE 4A3JF 5BYHE 3S1MF 4XLPE 4Q4ZE 2A6HE 4LLGE 4A3EF 2A6EE 1Y1WF 3GTMF 2JA8F 3H0GF 4A3KF 2O5IE 3GTOF 3S2HF 3HOWF 4A3GF 2Y0SI 1QKLA 5FJ8F 3S2DF 1R9TF 1TWGF 3HOVF 5M5XF 3H3VG 3S1QF 4MEYE 3S17F 4KN7E 4YFNE 3S14F 5FLMF 4BBRF 3RZOF 4A3FF 5IYBF 1YNNK 3EQLE 4C3HF 3GTJF 3PO3F 5C4XF 2R7ZF 1Y1VF 4OIPE 1WCMF 1TWHF 3GTGF 1YNJK 4YFXE 1SFOF 2JA5F 4C3JF 4GZYE 4BXXF 5TMCE 4A3MF 2NVXF 2A68E 5IP9F 3FKIF 2VUMF 2NVQF 4XLNE 2B63F 2WB1I 3GTPF 4YG2E 4A3BF 2CW0E 4OIQE 4XSXE 4C3IF 5M5WF 4AYBK 4MQ9E 2JA6F 4A3LF 5D4CE 4OINE 4KMUE 1I6VE 4C2MF 5C3EF 4G7HE 3S1RF 2NVTF 1ZYRE 2A69E 1K83F 1TWCF 3S15F 1HQME 3I4NF 3HOZF 4BY1F 1I50F 4KN4E 4Q5SE 4LK0E 5M5YF 2E2JF 4G7ZE 2YU9F 1TWFF 3WODE 3I4MF 4LJZE 2R93F 4YFKE 5M3MF 5E18E 1I3QF 5C44F 3HOUF 2O5JE 2WAQK 3S1NF 2JA7F 3GTLF 5IP7F 4JK1E 3GTQF 2NVYF 4XSZE 5C4JF 4OIOE 4X6AF 5IPLE 3CQZF 1I6HF 3GTKF
chains in the Genus database with same CATH superfamily
1SMYE 4BY1E 5E17E 4A3CE 1IW7E 3HKZK 5IYDF 2E2HF 4A93F 5D4DE 4A3IE 5M3FE 3RZDF 4OIRE 2E2JE 3K7AF 4Y7NE 3M3YF 2BE5E 3I4ME 4BBSE 3S16E 4A3CF 2R93E 4A3IF 5M3FF 5M3ME 1TWAE 3HOUE 3DXJE 4ZH4E 4A3DE 4Y52E 3S1NE 3PO2E 4Y7NF 3GTLE 5TMFE 4BBSF 5IYCE 3S16F 4X6AE 4AYBH 5D4EE 3M4OE 4BY7E 1TWAF 4Y52F 3HOXE 4A3DF 3HOYE 3PO2F 3GTKE 2E2IF 2R92E 4A3JE 5IYCF 3S1ME 2E2HE 4A93E 2PMZK 4LK1E 4A3EE 3RZDE 4BY7F 3M4OF 3HOXF 3HOYF 1Y1WE 4G7OE 3GTME 2R92F 4MEXE 2JA8E 2PPBE 3M3YE 3H0GE 4A3JF 5BYHE 1DZFA 3S1MF 4A3KE 4XLPE 4Q4ZE 2A6HE 4LLGE 4A3EF 3GTOE 3HOWE 3S2HE 4A3GE 2A6EE 5FJ8E 1Y1WF 3S2DE 3GTMF 3I4NE 1TWGE 2JA8F 5M5XE 3S1QE 3H0GF 3S17E 4A3KF 3S14E 2O5IE 3GTOF 3S2HF 3HOWF 4A3GF 4BBRE 3RZOE 2Y0SI 1QKLA 5FJ8F 3S2DF 2KRXA 1R9TF 4A3FE 2E2IE 1TWGF 3GTJE 5M5XF 3H3VG 3HOVF 3PO3E 4MEYE 3S1QF 3S17F 4KN7E 4YFNE 2R7ZE 2WAQH 3S14F 5FLMF 4BBRF 3RZOF 1WCME 3GTGE 4A3FF 4QIWH 1YNNK 3EQLE 4C3HF 5IYBF 3GTJF 1SFOE 2JA5E 4C3JE 3PO3F 4BXXE 4A3ME 2NVXE 2R7ZF 1Y1VF 4OIPE 3FKIE 1WCMF 1TWHF 2Y0SH 1YNJK 2VUME 3GTGF 4YFXE 1SFOF 2JA5F 4GZYE 4C3JF 2B63E 3GTPE 5TMCE 4A3MF 2NVXF 2A68E 5IP9F 4A3BE 4BXXF 3FKIF 2VUMF 4C3IE 1R9TE 5M5WE 2NVQF 3HOVE 4XLNE 2JA6E 2B63F 2WB1I 3GTPF 4YG2E 4A3BF 2CW0E 4OIQE 4XSXE 5FLME 4C3IF 5M5WF 4AYBK 4C2ME 4MQ9E 4C3HE 5IYBE 2JA6F 5C3EE 3S1RE 3H3VF 2NVTE 5D4CE 4OINE 4A3LF 1Y1VE 4KMUE 1K83E 5C4XF 1TWHE 5C4XE 1I6VE 4C2MF 5C3EF 4G7HE 3S1RF 3HOZE 2NVTF 2WB1H 1I50E 5IP9E 1ZYRE 2A69E 1K83F 1TWCF 5M5YE 2NVQE 2YU9E 1TWFE 1HQME 3HKZH 3I4NF 3S15F 3HOZF 1EIKA 4BY1F 1I50F 4KN4E 4Q5SE 4LK0E 1I3QE 5M5YF 5C44E 4G7ZE 2E2JF 2YU9F 1TWFF 2JA7E 3WODE 5IP7E 3I4MF 4A3LE 3GTQE 2NVYE 4LJZE 5C4JE 2R93F 4YFKE 5M3MF 3CQZE 1I3QF 5E18E 5C44F 3HOUF 2WAQK 3S1NF 1I6HE 2O5JE 2JA7F 3GTLF 5IP7F 4JK1E 3GTQF 2NVYF 4QIWK 4XSZE 5C4JF 5IYDE 4OIOE 4X6AF 5IPLE 3CQZF 1TWCE 3K7AE 1I6HF 3S15E 3GTKF 2PMZH
chains in the Genus database with same CATH topology
1SMYE 5E17E 1IW7E 3HKZK 5IYDF 2E2HF 4A93F 5D4DE 4OIRE 3RZDF 3K7AF 3M3YF 2BE5E 4A3CF 4A3IF 5M3FF 3DXJE 4ZH4E 4Y7NF 5TMFE 4BBSF 3S16F 5D4EE 1TWAF 4Y52F 4A3DF 3PO2F 2E2IF 5IYCF 2PMZK 4LK1E 3M4OF 4BY7F 3HOXF 3HOYF 4G7OE 2R92F 4MEXE 2PPBE 4A3JF 5BYHE 3S1MF 4XLPE 4Q4ZE 2A6HE 4LLGE 4A3EF 2A6EE 1Y1WF 3GTMF 2JA8F 3H0GF 4A3KF 2O5IE 3GTOF 3S2HF 3HOWF 4A3GF 2Y0SI 1QKLA 5FJ8F 3S2DF 2KRXA 1R9TF 1TWGF 3HOVF 5M5XF 3H3VG 3S1QF 4MEYE 3S17F 4KN7E 4YFNE 3S14F 5FLMF 4BBRF 3RZOF 4A3FF 5IYBF 1YNNK 3EQLE 4C3HF 3GTJF 3PO3F 5C4XF 2R7ZF 1Y1VF 4OIPE 1WCMF 1TWHF 3GTGF 1YNJK 4YFXE 1SFOF 2JA5F 4C3JF 4GZYE 4BXXF 5TMCE 4A3MF 2NVXF 2A68E 5IP9F 3FKIF 2VUMF 2NVQF 4XLNE 2B63F 2WB1I 3GTPF 4YG2E 4A3BF 2CW0E 4OIQE 4XSXE 4C3IF 5M5WF 4AYBK 4MQ9E 2JA6F 4A3LF 5D4CE 4OINE 4KMUE 1I6VE 4C2MF 5C3EF 4G7HE 3S1RF 2NVTF 1ZYRE 2A69E 1K83F 1TWCF 3S15F 1HQME 3I4NF 3HOZF 4BY1F 1I50F 4KN4E 4Q5SE 4LK0E 5M5YF 2E2JF 4G7ZE 2YU9F 1TWFF 3WODE 3I4MF 4LJZE 2R93F 4YFKE 5M3MF 5E18E 1I3QF 5C44F 3HOUF 2O5JE 2WAQK 3S1NF 2JA7F 3GTLF 5IP7F 4JK1E 3GTQF 2NVYF 4QIWK 4XSZE 5C4JF 4OIOE 4X6AF 5IPLE 3CQZF 1I6HF 3GTKF
chains in the Genus database with same CATH homology


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