4A3CF

Rna polymerase ii initial transcribing complex with a 5nt dna-rna hybrid
Total Genus 29
Loading diagram...

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
29
sequence length
84
structure length
84
Chain Sequence
KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
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 Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
molecule tags Transcription
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
total genus 29
structure length 84
sequence length 84
ec nomenclature
pdb deposition date 2011-09-30

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 4a3cF00
4XSZE 3HKZK 4A3JF 4C2MF 5C3EF 4Y52F 3CQZF 2CW0E 2B63F 3H3VG 1TWHF 4BBRF 4OIQE 4A3IF 5D4CE 3HOXF 2PPBE 2VUMF 4A3CF 5IP7F 2NVTF 4Q5SE 1I6VE 4GZYE 4A3GF 4G7ZE 3S1MF 2PMZK 5C4XF 4C3JF 4BY7F 2WB1I 3GTKF 2NVXF 4A3DF 3GTOF 4ZH4E 3FKIF 3GTJF 4MEXE 3S1RF 5E17E 4Y7NF 3GTPF 3S17F 4LLGE 4A3EF 4X6AF 2JA8F 4OINE 4KN7E 3M3YF 3DXJE 4XLPE 1WCMF 4YFKE 1R9TF 1SMYE 5M5WF 2JA6F 1TWGF 4C3HF 3HOZF 5M3MF 3S1QF 3HOUF 4OIOE 5IYDF 4A3BF 2BE5E 5TMFE 4A3LF 1IW7E 5IPLE 4XLNE 4LJZE 2R93F 4YG2E 3WODE 4LK1E 4MQ9E 4JK1E 4A3MF 3K7AF 4A3FF 4YFXE 3H0GF 2NVYF 4XSXE 2NVQF 3EQLE 3S2DF 5IP9F 4OIPE 4G7HE 2JA7F 5C4JF 3PO2F 3S14F 2E2HF 2O5JE 1Y1VF 1SFOF 3S2HF 3HOYF 3PO3F 2Y0SI 1QKLA 1HQME 4OIRE 2R92F 1I3QF 1Y1WF 3GTMF 4MEYE 2A69E 2A6HE 4KN4E 2R7ZF 3RZOF 1ZYRE 3GTQF 4C3IF 2A6EE 5D4DE 5M3FF 3HOVF 3I4NF 4BY1F 4G7OE 4A93F 5FJ8F 1TWFF 3I4MF 4LK0E 5TMCE 5C44F 5E18E 4KMUE 5D4EE 5BYHE 5FLMF 5M5YF 1TWAF 3S1NF 1I50F 1K83F 2E2JF 4BBSF 4BXXF 5IYCF 1I6HF 3GTLF 2E2IF 2A68E 4A3KF 2O5IE 3M4OF 4YFNE 4AYBK 3S15F 3HOWF 1YNJK 2JA5F 2YU9F 1TWCF 1YNNK 2WAQK 4Q4ZE 5M5XF 3RZDF 3GTGF 3S16F 5IYBF
chains in the Genus database with same CATH superfamily
5M3ME 4XSZE 3HKZK 5FJ8E 1DZFA 5M5XE 4A3JF 3I4ME 4C2MF 5C3EF 4Y52F 3CQZF 2CW0E 4QIWK 2B63F 3H3VG 2KRXA 1TWHF 4BBRF 4OIQE 5FLME 5D4CE 3HOXF 4A3IF 2PPBE 2VUMF 5IP7F 2NVTF 3S1QE 4A3CF 4Q5SE 1K83E 1I6VE 4GZYE 4A3GF 3GTQE 4G7ZE 3HKZH 3S1MF 2PMZK 4A3FE 2PMZH 4C3JF 5C4XF 3GTOE 4BY7F 3S15E 2WB1I 2WAQH 3GTKF 5IP9E 2NVXF 4A3DF 3GTOF 4ZH4E 3FKIF 3S17E 3GTJF 4MEXE 3S1RF 5E17E 4Y7NF 3H0GE 3GTPF 1Y1VE 3FKIE 4LLGE 4A3EF 3GTJE 3S17F 4X6AF 2JA8F 4OINE 4AYBH 2JA7E 4KN7E 5C4JE 4A3EE 4X6AE 3HOZE 3M3YF 2WB1H 2YU9E 3DXJE 4Y52E 4XLPE 1WCMF 2B63E 4YFKE 1R9TF 1SMYE 1I50E 5M5WF 2JA6F 1TWGF 4C3HF 3HOZF 2R92E 5M3MF 3HOXE 2VUME 3S1QF 4A3LE 3HOUF 4OIOE 5IYDF 4A3BF 2E2HE 2BE5E 5TMFE 3CQZE 4A3LF 1IW7E 5IPLE 3S1NE 4XLNE 1I3QE 4LJZE 2R7ZE 2R93F 4YG2E 3WODE 4LK1E 3GTKE 4MQ9E 4JK1E 2E2IE 4A3KE 4A3MF 3K7AF 4A3FF 4C3JE 4YFXE 3H0GF 2NVYF 3GTPE 4C3IE 4XSXE 2NVQF 3EQLE 2JA5E 4BY1E 3S2DF 5IP9F 2NVXE 4A3DE 4OIPE 4G7HE 2JA7F 5C4JF 5M3FE 3S14F 3RZDE 2E2HF 3PO2F 3S16E 3HOYE 3S2HE 2O5JE 1WCME 1Y1VF 1R9TE 1SFOF 3S2HF 3HOYF 3PO3F 2Y0SI 1QKLA 1HQME 5IYBE 5IP7E 4OIRE 5IYCE 1TWGE 1I3QF 4C3HE 5C3EE 2R92F 5M5YE 3GTLE 2R93E 1TWAE 1Y1WF 3GTMF 3M4OE 4MEYE 2A69E 2A6HE 2NVTE 3K7AE 4BXXE 4KN4E 1I6HE 2R7ZF 3RZOF 1ZYRE 3GTQF 4C3IF 5C4XE 4Y7NE 3RZOE 3HOVE 2A6EE 3I4NE 5D4DE 5M3FF 3PO2E 3HOVF 3I4NF 1TWCE 4QIWH 4BY1F 3S2DE 3S1RE 3M3YE 4G7OE 4A93F 5FJ8F 1TWFF 3I4MF 4LK0E 5M5WE 5TMCE 5C44F 2JA8E 5E18E 4KMUE 5D4EE 3HOUE 5BYHE 3GTGE 1TWHE 5C44E 2E2JE 5FLMF 4A3IE 5M5YF 2Y0SH 1TWAF 1Y1WE 3PO3E 3S1NF 1I50F 2JA6E 4C2ME 1K83F 2E2JF 4BBSF 3H3VF 1EIKA 4BXXF 5IYDE 5IYCF 1I6HF 4BBRE 3GTLF 2E2IF 4A3BE 2A68E 4A3KF 4A3ME 2O5IE 4BBSE 4A3CE 3GTME 3M4OF 4YFNE 4A3GE 2NVYE 3S1ME 4AYBK 3HOWE 3S15F 4BY7E 3S14E 3HOWF 4A93E 1YNJK 1TWFE 2NVQE 1SFOE 2JA5F 2YU9F 1TWCF 1YNNK 2WAQK 4Q4ZE 4A3JE 5M5XF 3RZDF 3GTGF 3S16F 5IYBF
chains in the Genus database with same CATH topology
4XSZE 3HKZK 4A3JF 4C2MF 5C3EF 4Y52F 3CQZF 2CW0E 4QIWK 2B63F 3H3VG 2KRXA 1TWHF 4BBRF 4OIQE 4A3IF 5D4CE 3HOXF 2PPBE 2VUMF 4A3CF 5IP7F 2NVTF 4Q5SE 1I6VE 4GZYE 4A3GF 4G7ZE 3S1MF 2PMZK 5C4XF 4C3JF 4BY7F 2WB1I 3GTKF 2NVXF 4A3DF 3GTOF 4ZH4E 3FKIF 3GTJF 4MEXE 3S1RF 5E17E 4Y7NF 3GTPF 3S17F 4LLGE 4A3EF 4X6AF 2JA8F 4OINE 4KN7E 3M3YF 3DXJE 4XLPE 1WCMF 4YFKE 1R9TF 1SMYE 5M5WF 2JA6F 1TWGF 4C3HF 3HOZF 5M3MF 3S1QF 3HOUF 4OIOE 5IYDF 4A3BF 2BE5E 5TMFE 4A3LF 1IW7E 5IPLE 4XLNE 4LJZE 2R93F 4YG2E 3WODE 4LK1E 4MQ9E 4JK1E 4A3MF 3K7AF 4A3FF 4YFXE 3H0GF 2NVYF 4XSXE 2NVQF 3EQLE 3S2DF 5IP9F 4OIPE 4G7HE 2JA7F 5C4JF 3PO2F 3S14F 2E2HF 2O5JE 1Y1VF 1SFOF 3S2HF 3HOYF 3PO3F 2Y0SI 1QKLA 1HQME 4OIRE 2R92F 1I3QF 1Y1WF 3GTMF 4MEYE 2A69E 2A6HE 4KN4E 2R7ZF 3RZOF 1ZYRE 3GTQF 4C3IF 2A6EE 5D4DE 5M3FF 3HOVF 3I4NF 4BY1F 4G7OE 4A93F 5FJ8F 1TWFF 3I4MF 4LK0E 5TMCE 5C44F 5E18E 4KMUE 5D4EE 5BYHE 5FLMF 5M5YF 1TWAF 3S1NF 1I50F 1K83F 2E2JF 4BBSF 4BXXF 5IYCF 1I6HF 3GTLF 2E2IF 2A68E 4A3KF 2O5IE 3M4OF 4YFNE 4AYBK 3S15F 3HOWF 1YNJK 2JA5F 2YU9F 1TWCF 1YNNK 2WAQK 4Q4ZE 5M5XF 3RZDF 3GTGF 3S16F 5IYBF
chains in the Genus database with same CATH homology


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