3S1QF

Rna polymerase ii initiation complex with a 5-nt 3'-deoxy rna soaked with atp
Total Genus 22
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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
22
sequence length
85
structure length
85
Chain Sequence
EKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
Loading diagram...

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 Initiation complex structure and promoter proofreading.
pubmed doi rcsb
molecule tags Transcription/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 22
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 3s1qF00
2A68E 1TWHF 4XLNE 4C2MF 3S17F 3S2DF 4A93F 5C4XF 3FKIF 3HOZF 2Y0SI 3S1RF 3S2HF 4KMUE 1TWFF 2E2HF 3I4NF 3HKZK 4A3EF 2E2IF 2WAQK 4LLGE 3S15F 4XSZE 4A3MF 5M3FF 4A3LF 1IW7E 4AYBK 4OIQE 4C3HF 5IPLE 1R9TF 4OIOE 2JA8F 3HOUF 4BY7F 3HOYF 4BBSF 5BYHE 3HOVF 5C44F 2NVXF 2JA5F 3GTLF 2R93F 4Q5SE 4YG2E 5IYBF 4LK1E 2E2JF 1QKLA 4OIPE 2BE5E 5M5WF 1I6HF 4A3KF 2R7ZF 1TWAF 1K83F 4MEYE 2YU9F 3GTKF 5FLMF 4Q4ZE 5IYDF 4OIRE 2NVTF 4ZH4E 4YFNE 5D4EE 4A3FF 2B63F 3S1MF 2NVYF 2CW0E 4A3CF 2A6HE 4A3JF 4XSXE 4JK1E 3DXJE 5FJ8F 1WCMF 5TMCE 4MQ9E 5C4JF 5IP9F 4LJZE 1YNNK 5M3MF 3S1NF 3I4MF 3PO2F 4Y52F 4OINE 4A3BF 2R92F 2WB1I 5TMFE 1I3QF 4C3IF 3GTGF 4KN4E 2PPBE 5E17E 1TWGF 5D4DE 1ZYRE 2A69E 4G7HE 3RZDF 3K7AF 1SFOF 2NVQF 4MEXE 5D4CE 3S14F 5E18E 3M4OF 4A3IF 1I50F 4G7OE 3M3YF 4X6AF 3GTQF 4C3JF 4BBRF 3S16F 3HOXF 5M5YF 3H3VG 1Y1VF 4A3DF 2PMZK 3WODE 1I6VE 1SMYE 3GTMF 1Y1WF 4LK0E 1HQME 3PO3F 2O5IE 4YFKE 5M5XF 3S1QF 3CQZF 4BXXF 1YNJK 3EQLE 2VUMF 4KN7E 5IP7F 4G7ZE 3GTJF 3HOWF 4XLPE 2A6EE 4BY1F 4GZYE 4Y7NF 1TWCF 5C3EF 2JA6F 2O5JE 4YFXE 3GTPF 3GTOF 4A3GF 5IYCF 3RZOF 2JA7F 3H0GF
chains in the Genus database with same CATH superfamily
2A68E 1TWHF 5M3ME 4XLNE 4C2MF 3S17F 4A3FE 2B63E 3S2DF 4A93F 2NVTE 5C4XF 3FKIF 3HOZF 2Y0SI 1K83E 3S1RF 1TWHE 3H0GE 2E2HE 2JA8E 4KMUE 1TWFF 2E2HF 3S2HF 3CQZE 3I4NF 3HOZE 3HKZK 4A3EF 2E2IF 2WAQK 4LLGE 3PO3E 4XSZE 3S15F 3S2HE 2Y0SH 3GTPE 1I6HE 4QIWK 4A3MF 5M3FF 4X6AE 4A3LE 4A3LF 1IW7E 4AYBK 3GTKE 4OIQE 4C3HF 3M4OE 3GTOE 5IPLE 1R9TF 2VUME 1TWFE 4OIOE 3RZOE 2JA8F 1EIKA 4BY7E 3HOUF 4BY7F 2E2JE 3FKIE 3HOYF 4BBSF 5BYHE 3HOVF 5C44F 1DZFA 2NVXF 3S17E 2JA5F 3GTLF 3PO2E 3GTJE 4C3HE 2R93F 2JA7E 4Q5SE 4BY1E 4YG2E 5IYBF 4LK1E 2E2JF 1QKLA 4OIPE 5M5YE 2BE5E 1R9TE 5M5WF 1I6HF 1WCME 4A3KF 2R7ZF 3GTQE 1TWAF 3I4NE 1K83F 4MEYE 2YU9F 3GTKF 5FLMF 4Q4ZE 4Y7NE 1I50E 5IYDF 4A3CE 4OIRE 2NVTF 4ZH4E 5C4XE 4YFNE 5D4EE 4A3FF 2B63F 3GTME 3S1MF 2NVYF 3S16E 2CW0E 2YU9E 4A3CF 2A6HE 1Y1VE 4A3DE 4A3JF 4XSXE 4JK1E 3DXJE 3RZDE 4BXXE 5FJ8F 3HOXE 1WCMF 5TMCE 4MQ9E 5M5XE 5C4JF 5IYBE 4A93E 5IP9F 4LJZE 1YNNK 4C2ME 5M3MF 3S1NF 4QIWH 4A3IE 1SFOE 2JA6E 3I4MF 4Y52F 4OINE 4A3BF 1TWAE 3PO2F 2R92F 2WB1I 5TMFE 1I3QF 3S14E 4C3IF 5M5WE 4KN4E 3GTGF 4BBRE 3HOWE 4BBSE 4C3JE 5IP7E 2PPBE 5E17E 1TWGF 5D4DE 1TWGE 1ZYRE 2A69E 4G7HE 3RZDF 2R93E 2PMZH 3K7AF 1SFOF 2NVQF 2WB1H 4MEXE 5D4CE 5C3EE 2JA5E 3GTLE 3S14F 5E18E 3M4OF 1Y1WE 3HOYE 4A3IF 1I50F 5IYDE 3I4ME 4A3ME 3M3YF 3HOUE 4G7OE 4X6AF 5IP9E 5FJ8E 2KRXA 3GTQF 4C3JF 4BBRF 3S16F 3HOXF 3S1ME 2R92E 5M5YF 3H3VG 4AYBH 4A3JE 1Y1VF 4A3DF 2PMZK 3WODE 3S1NE 5M3FE 3S2DE 2NVYE 1I6VE 1SMYE 3GTMF 1Y1WF 4LK0E 1HQME 3S15E 2O5IE 4A3EE 4YFKE 5M5XF 5C44E 4A3KE 5FLME 2E2IE 3PO3F 3S1QF 3CQZF 4BXXF 5IYCE 3S1RE 1YNJK 2R7ZE 3EQLE 2VUMF 4KN7E 5IP7F 3M3YE 4G7ZE 3GTJF 3HOWF 4XLPE 2A6EE 4C3IE 3GTGE 4BY1F 2NVXE 4GZYE 4Y7NF 3HOVE 4A3BE 1TWCF 5C3EF 1TWCE 2JA6F 3K7AE 2NVQE 2O5JE 4YFXE 4A3GE 3GTPF 3HKZH 5C4JE 2WAQH 3GTOF 4A3GF 5IYCF 1I3QE 3RZOF 2JA7F 3H0GF 3H3VF 3S1QE 4Y52E
chains in the Genus database with same CATH topology
2A68E 1TWHF 4XLNE 4C2MF 3S17F 3S2DF 4A93F 5C4XF 3FKIF 3HOZF 2Y0SI 3S1RF 3S2HF 4KMUE 1TWFF 2E2HF 3I4NF 3HKZK 4A3EF 2E2IF 2WAQK 4LLGE 3S15F 4XSZE 4QIWK 4A3MF 5M3FF 4A3LF 1IW7E 4AYBK 4OIQE 4C3HF 5IPLE 1R9TF 4OIOE 2JA8F 3HOUF 4BY7F 3HOYF 4BBSF 5BYHE 3HOVF 5C44F 2NVXF 2JA5F 3GTLF 2R93F 4Q5SE 4YG2E 5IYBF 4LK1E 2E2JF 1QKLA 4OIPE 2BE5E 5M5WF 1I6HF 4A3KF 2R7ZF 1TWAF 1K83F 4MEYE 2YU9F 3GTKF 5FLMF 4Q4ZE 5IYDF 4OIRE 2NVTF 4ZH4E 4YFNE 5D4EE 4A3FF 2B63F 3S1MF 2NVYF 2CW0E 4A3CF 2A6HE 4A3JF 4XSXE 4JK1E 3DXJE 5FJ8F 1WCMF 5TMCE 4MQ9E 5C4JF 5IP9F 4LJZE 1YNNK 5M3MF 3S1NF 3I4MF 3PO2F 4Y52F 4OINE 4A3BF 2R92F 2WB1I 5TMFE 1I3QF 4C3IF 3GTGF 4KN4E 2PPBE 5E17E 1TWGF 5D4DE 1ZYRE 2A69E 4G7HE 3RZDF 3K7AF 1SFOF 2NVQF 4MEXE 5D4CE 3S14F 5E18E 3M4OF 4A3IF 1I50F 4G7OE 3M3YF 4X6AF 2KRXA 3GTQF 4C3JF 4BBRF 3S16F 3HOXF 5M5YF 3H3VG 1Y1VF 4A3DF 2PMZK 3WODE 1I6VE 1SMYE 3GTMF 1Y1WF 4LK0E 1HQME 3PO3F 2O5IE 4YFKE 5M5XF 3S1QF 3CQZF 4BXXF 1YNJK 3EQLE 2VUMF 4KN7E 5IP7F 4G7ZE 3GTJF 3HOWF 4XLPE 2A6EE 4BY1F 4GZYE 4Y7NF 1TWCF 5C3EF 2JA6F 2O5JE 4YFXE 3GTPF 3GTOF 4A3GF 5IYCF 3RZOF 2JA7F 3H0GF
chains in the Genus database with same CATH homology


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