4A3GE

Rna polymerase ii initial transcribing complex with a 2nt dna-rna hybrid
Total Genus 63
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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
63
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 63
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 4a3gE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 4a3gE02
3S1NE 5M5XE 4X6AE 2E2HE 5C3EE 2VUME 2NVQE 3GTKE 5M3FE 1I50E 3S1ME 1SFOE 1TWFE 4BY7E 1R9TE 3RZOE 1Y1WE 5C4XE 3S14E 4BY1E 3S16E 2WAQH 3S2DE 3HKZH 1WCME 2WB1H 3S17E 1Y1VE 3GTOE 4A3KE 3S1QE 1TWHE 4BBRE 3I4NE 4QIWH 4A3ME 4BXXE 4A3JE 3HOVE 4AYBH 2NVXE 3GTJE 4C3JE 3GTGE 1TWGE 4A3IE 2JA8E 3M3YE 3PO2E 3CQZE 3FKIE 5M5WE 5IP7E 4A3GE 5IYDE 4C3HE 4A3CE 2R7ZE 3HOUE 2YU9E 3GTQE 2Y0SH 3H3VF 2NVTE 3GTPE 4A3DE 5C44E 4Y52E 3RZDE 4A3LE 5IYBE 5M5YE 3I4ME 2E2JE 3H0GE 4Y7NE 1TWAE 1DZFA 5FLME 5M3ME 5C4JE 4BBSE 2PMZH 1EIKA 1K83E 3GTME 5FJ8E 3HOYE 4C2ME 3GTLE 2B63E 3S15E 1I6HE 3HOZE 2JA5E 3PO3E 1TWCE 2R93E 4C3IE 3S2HE 2JA7E 2NVYE 4A3BE 5IP9E 4A3FE 4A3EE 3S1RE 5IYCE 1I3QE 3HOWE 3HOXE 2JA6E 2R92E 3K7AE 4A93E 3M4OE 2E2IE
chains in the Genus database with same CATH superfamily
1SFOF 4BY7F 2PMZK 3S1NE 1R9TF 5TMFE 3DXJE 3RZOF 4A3BF 5D4CE 5C4XF 5M5XE 3S1RF 3S14F 4BY1F 4X6AE 2E2HE 5IYCF 5C3EE 2VUME 2NVQE 3GTKE 3S2DF 5M3FE 4LK0E 1I50E 3S1ME 1SFOE 1TWFE 4BY7E 1R9TE 3RZOE 1WCMF 4MQ9E 2JA6F 1Y1WE 5C4XE 1ZYRE 3S14E 4BY1E 3S16E 2CW0E 2WAQH 4YFNE 3M4OF 2WB1I 4KMUE 5D4DE 2E2IF 3S2DE 2KRXA 3HKZH 1Y1VF 3S17F 3S1NF 3GTOF 4A3KF 3S1QF 1TWHF 4G7OE 3I4NF 4BXXF 1WCME 4A3JF 3HOVF 5M3FF 2NVXF 1TWFF 3GTJF 4C3JF 2WB1H 3S17E 1Y1VE 4YFXE 3GTOE 4A3KE 3S1QE 4KN4E 1TWHE 4OIPE 4BBRE 1TWGF 1YNNK 4A3IF 3I4NE 4QIWH 4A3ME 1Y1WF 1HQME 4BXXE 2JA8F 3M3YF 4A3JE 3PO2F 3CQZF 3HOVE 3FKIF 5D4EE 5M5WF 4AYBH 5IP7F 2NVXE 3GTJE 4C3JE 4XLNE 5IYDF 4JK1E 4C3HF 4A3GF 4LLGE 4A3CF 3GTGE 1TWGE 4A3IE 2JA8E 3M3YE 4OIOE 2YU9F 3PO2E 3EQLE 4KN7E 3CQZE 3FKIE 5M5WE 3GTQF 5IP7E 2PPBE 1YNJK 2NVTF 3GTPF 3H3VG 4A3GE 1IW7E 4BBRF 5IYDE 4C3HE 3HKZK 4A3DF 2O5JE 4A3MF 4A3CE 2R7ZE 4Y52F 4OIQE 3RZDF 4XSZE 1QKLA 5IYBF 4A3LF 4YG2E 5M5YF 3HOUE 2YU9E 4Q5SE 2E2JF 3I4MF 3GTQE 4Y7NF 2Y0SH 3H3VF 2NVTE 3GTPE 4A3DE 3GTGF 2O5IE 5C44E 4Y52E 3RZDE 2A6HE 4A3LE 2A69E 5IYBE 4QIWK 4OIRE 4BBSF 5M5YE 3I4ME 2A6EE 4LK1E 2E2JE 3H0GE 1K83F 5M3MF 4Y7NE 5C4JF 3GTMF 4G7ZE 5FJ8F 4OINE 2R7ZF 1TWAE 3HOYF 1DZFA 5E18E 2B63F 3S15F 5IPLE 4GZYE 3HOUF 3HOZF 2BE5E 2Y0SI 2WAQK 2JA5F 5FLME 5M3ME 5C4JE 4BBSE 2PMZH 3PO3F 1EIKA 1K83E 1TWCF 3GTME 2R93F 4MEXE 5FJ8E 4C3IF 3HOYE 3S2HF 5C44F 4XSXE 4C2ME 2NVYF 5TMCE 2JA7F 3GTLE 2B63E 3S15E 1I6HE 5IP9F 4Q4ZE 4A3FF 4A3EF 3HOZE 3H0GF 4G7HE 5E17E 2JA5E 3PO3E 1I6VE 1TWAF 3WODE 1TWCE 1I3QF 2R93E 1SMYE 4C3IE 3S2HE 4YFKE 3HOWF 2JA7E 2NVYE 4A3BE 3HOXF 2R92F 5IP9E 4A3FE 3K7AF 4A3EE 5FLMF 3S1RE 4A93F 5IYCE 3S16F 4AYBK 4XLPE 4C2MF 5BYHE 1I3QE 3GTLF 3HOWE 5M5XF 1I6HF 4ZH4E 4X6AF 2E2HF 2A68E 3HOXE 2JA6E 2R92E 3K7AE 4LJZE 5C3EF 2VUMF 4A93E 4MEYE 2NVQF 3GTKF 3M4OE 1I50F 2E2IE 3S1MF
chains in the Genus database with same CATH topology
3S1NE 5M5XE 4X6AE 2E2HE 5C3EE 2VUME 2NVQE 3GTKE 5M3FE 1I50E 3S1ME 1SFOE 1TWFE 4BY7E 1R9TE 3RZOE 1Y1WE 5C4XE 3S14E 4BY1E 3S16E 2WAQH 3S2DE 3HKZH 1WCME 2WB1H 3S17E 1Y1VE 3GTOE 4A3KE 3S1QE 1TWHE 4BBRE 3I4NE 4QIWH 4A3ME 4BXXE 4A3JE 3HOVE 4AYBH 2NVXE 3GTJE 4C3JE 3GTGE 1TWGE 4A3IE 2JA8E 3M3YE 3PO2E 3CQZE 3FKIE 5M5WE 5IP7E 4A3GE 5IYDE 4C3HE 4A3CE 2R7ZE 3HOUE 2YU9E 3GTQE 2Y0SH 3H3VF 2NVTE 3GTPE 4A3DE 5C44E 4Y52E 3RZDE 4A3LE 5IYBE 5M5YE 3I4ME 2E2JE 3H0GE 4Y7NE 1TWAE 1DZFA 5FLME 5M3ME 5C4JE 4BBSE 2PMZH 1EIKA 1K83E 3GTME 5FJ8E 3HOYE 4C2ME 3GTLE 2B63E 3S15E 1I6HE 3HOZE 2JA5E 3PO3E 1TWCE 2R93E 4C3IE 3S2HE 2JA7E 2NVYE 4A3BE 5IP9E 4A3FE 4A3EE 3S1RE 5IYCE 1I3QE 3HOWE 3HOXE 2JA6E 2R92E 3K7AE 4A93E 3M4OE 2E2IE
chains in the Genus database with same CATH homology


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