4A3IE

Rna polymerase ii binary complex with dna
Total Genus 60
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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
60
sequence length
214
structure length
214
Chain Sequence
DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
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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
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
total genus 60
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2011-09-30

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
E PF01191 RNA_pol_Rpb5_C RNA polymerase Rpb5, C-terminal domain
E PF03871 RNA_pol_Rpb5_N RNA polymerase Rpb5, N-terminal domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1340.10 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 RNA polymerase, Rpb5, N-terminal domain 4a3iE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 4a3iE02
3I4ME 3S15E 4BBSE 1I3QE 3HOZE 1I50E 3S2HE 4C3HE 3S1QE 2NVYE 2R92E 1SFOE 5C44E 4Y7NE 5M5XE 3S2DE 2B63E 1K83E 4AYBH 2R7ZE 3FKIE 5M5YE 1WCME 3HOWE 3GTME 3GTQE 4A3LE 3I4NE 3GTJE 2E2JE 2NVXE 4C3JE 3GTPE 3S1NE 3H3VF 4BBRE 3GTLE 3H0GE 3HOVE 4A3IE 4A3CE 2JA7E 1Y1WE 1TWHE 3CQZE 3GTKE 3HOYE 5IP7E 5FLME 3M3YE 4A3EE 4A3KE 3RZDE 4A3ME 1EIKA 5IYCE 3K7AE 3PO3E 4A3JE 4A3DE 3GTGE 3GTOE 3S14E 1DZFA 2JA5E 2E2HE 2R93E 3M4OE 4A93E 1TWCE 4A3GE 5IYDE 4QIWH 5IP9E 5M3ME 5IYBE 4C3IE 2E2IE 3RZOE 2PMZH 5C3EE 4BY1E 4A3BE 5FJ8E 3S17E 1R9TE 3HOUE 2YU9E 4X6AE 5M5WE 2VUME 4C2ME 5C4XE 3HKZH 3S1ME 1TWFE 3S16E 5M3FE 3PO2E 2WB1H 2Y0SH 2JA8E 1TWGE 2WAQH 4BY7E 4A3FE 3S1RE 4Y52E 2NVQE 4BXXE 1I6HE 2JA6E 1Y1VE 3HOXE 2NVTE 1TWAE 5C4JE
chains in the Genus database with same CATH superfamily
1ZYRE 3GTMF 3GTQF 4LJZE 4A3LF 3I4ME 3S15E 4BBSE 3GTJF 2E2JF 3I4NF 1I3QE 2NVXF 3H3VG 4C3JF 4YFKE 3GTPF 3S1NF 4GZYE 4AYBK 4BBRF 3HOZE 3GTLF 3H0GF 1I50E 4G7OE 3S2HE 3HOVF 4A3IF 4A3CF 4C3HE 4X6AF 3S1QE 2NVYE 2R92E 4G7ZE 1Y1WF 2JA7F 1TWHF 4LLGE 1SFOE 5C44E 4Y7NE 3CQZF 5IP7F 3GTKF 5FLMF 5M5XE 3S2DE 2A6EE 4A3KF 4A3EF 2B63E 4A3MF 3RZDF 1K83E 5IYCF 3K7AF 4MQ9E 3PO3F 4A3JF 4A3DF 4AYBH 2PMZK 4XSXE 3GTGF 2R7ZE 3FKIE 3GTOF 3HOUF 5M5YE 2JA5F 2R7ZF 3S14F 1WCME 3HOWE 4OIRE 2E2HF 4XLPE 2R93F 3M4OF 4A93F 3GTME 5E17E 3GTQE 4A3LE 1TWCF 4YG2E 4A3GF 3I4NE 3GTJE 5TMFE 2E2JE 5IYDF 2NVXE 4C3JE 3GTPE 3S1NE 5IP9F 3H3VF 4ZH4E 5M3MF 5IYBF 4BBRE 4C3IF 2E2IF 3RZOF 3GTLE 1YNJK 3HKZK 5C3EF 4OIQE 3H0GE 4OIOE 4BY1F 3HOVE 4A3IE 4A3CE 4MEYE 5TMCE 5FJ8F 4A3BF 2JA7E 1Y1WE 1TWHE 3S17F 2Y0SI 3CQZE 3GTKE 3HOYE 5IP7E 5FLME 3M3YE 4A3EE 4A3KE 1I6VE 4QIWK 3RZDE 4A3ME 5M5WF 2YU9F 5IYCE 2VUMF 4KN4E 2WAQK 4LK1E 3K7AE 5IPLE 1EIKA 4C2MF 3PO3E 4MEXE 3M3YF 4A3JE 4A3DE 5C4XF 4OINE 3GTGE 3GTOE 3S14E 1DZFA 3S1MF 2JA5E 3WODE 1TWFF 3S16F 2E2HE 5M3FF 2R93E 4XSZE 4OIPE 3M4OE 3PO2F 4A93E 4Q5SE 1TWCE 5BYHE 4A3GE 2JA8F 2BE5E 5IYDE 4BY7F 4Y52F 4A3FF 3S1RF 4QIWH 5IP9E 4Q4ZE 5M3ME 5IYBE 2NVQF 4C3IE 2E2IE 3RZOE 5D4DE 1I6HF 1Y1VF 2PMZH 2JA6F 2PPBE 5C3EE 4BXXF 4BY1E 3HOXF 2NVTF 1TWAF 1TWGF 4A3BE 2WB1I 5C4JF 5FJ8E 3I4MF 3S17E 3S15F 4JK1E 4BBSF 1I3QF 2A68E 1R9TE 3HOUE 2YU9E 1HQME 4X6AE 5M5WE 4LK0E 5D4EE 2VUME 4KMUE 2O5IE 3HOYF 1IW7E 3HOZF 4C2ME 1I50F 5C4XE 3HKZH 1QKLA 1YNNK 3S2HF 2A6HE 4C3HF 2O5JE 3S1ME 2A69E 2NVYF 2R92F 5D4CE 3S1QF 1TWFE 3S16E 2CW0E 5M3FE 3EQLE 4YFNE 4XLNE 4Y7NF 5C44F 1SFOF 3PO2E 5M5XF 3S2DF 2WB1H 4G7HE 2Y0SH 5E18E 2B63F 1K83F 4KN7E 2JA8E 1TWGE 2WAQH 4BY7E 4A3FE 3S1RE 4Y52E 2NVQE 1R9TF 4BXXE 3FKIF 1I6HE 2JA6E 1Y1VE 2KRXA 3DXJE 5M5YF 1WCMF 3HOWF 4YFXE 1SMYE 3HOXE 2NVTE 1TWAE 5C4JE
chains in the Genus database with same CATH topology
3I4ME 3S15E 4BBSE 1I3QE 3HOZE 1I50E 3S2HE 4C3HE 3S1QE 2NVYE 2R92E 1SFOE 5C44E 4Y7NE 5M5XE 3S2DE 2B63E 1K83E 4AYBH 2R7ZE 3FKIE 5M5YE 1WCME 3HOWE 3GTME 3GTQE 4A3LE 3I4NE 3GTJE 2E2JE 2NVXE 4C3JE 3GTPE 3S1NE 3H3VF 4BBRE 3GTLE 3H0GE 3HOVE 4A3IE 4A3CE 2JA7E 1Y1WE 1TWHE 3CQZE 3GTKE 3HOYE 5IP7E 5FLME 3M3YE 4A3EE 4A3KE 3RZDE 4A3ME 1EIKA 5IYCE 3K7AE 3PO3E 4A3JE 4A3DE 3GTGE 3GTOE 3S14E 1DZFA 2JA5E 2E2HE 2R93E 3M4OE 4A93E 1TWCE 4A3GE 5IYDE 4QIWH 5IP9E 5M3ME 5IYBE 4C3IE 2E2IE 3RZOE 2PMZH 5C3EE 4BY1E 4A3BE 5FJ8E 3S17E 1R9TE 3HOUE 2YU9E 4X6AE 5M5WE 2VUME 4C2ME 5C4XE 3HKZH 3S1ME 1TWFE 3S16E 5M3FE 3PO2E 2WB1H 2Y0SH 2JA8E 1TWGE 2WAQH 4BY7E 4A3FE 3S1RE 4Y52E 2NVQE 4BXXE 1I6HE 2JA6E 1Y1VE 3HOXE 2NVTE 1TWAE 5C4JE
chains in the Genus database with same CATH homology


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