4A3DE

Rna polymerase ii initial transcribing complex with a 6nt dna-rna hybrid
Total Genus 68
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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
68
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 68
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 4a3dE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 4a3dE02
1DZFA 4A3FE 5IP9E 3H3VF 3GTJE 2VUME 5C4JE 2NVYE 3HOVE 1TWGE 3S14E 3S1NE 3HKZH 4A3CE 2JA6E 5M5WE 5FJ8E 4Y52E 3H0GE 4BBRE 2E2HE 4A3BE 3K7AE 3S17E 3S16E 3M4OE 3PO2E 5IP7E 3RZDE 4BY1E 2PMZH 4Y7NE 4A93E 1R9TE 5M3FE 4A3KE 4QIWH 1I3QE 4C3IE 1K83E 1EIKA 4C2ME 4A3DE 5C44E 4A3ME 1TWCE 1Y1WE 3S2HE 4AYBH 2B63E 3HOXE 3PO3E 1TWAE 4BXXE 5C3EE 4A3LE 1Y1VE 5FLME 3GTOE 2NVXE 2NVQE 2E2JE 3S15E 3S1RE 3S1QE 3HOZE 4A3GE 3HOWE 5IYBE 3GTKE 1TWFE 2JA5E 2JA7E 2WAQH 3M3YE 3I4ME 1SFOE 3RZOE 2NVTE 3S1ME 4A3IE 2Y0SH 4A3EE 3HOUE 3GTME 4BY7E 3GTQE 3GTGE 4BBSE 2WB1H 4C3JE 3S2DE 4C3HE 3CQZE 3I4NE 5IYDE 4X6AE 3FKIE 1I6HE 2E2IE 5M5YE 1WCME 4A3JE 3GTPE 2R7ZE 3GTLE 2R92E 2YU9E 5C4XE 2R93E 3HOYE 1I50E 5M5XE 1TWHE 5IYCE 5M3ME 2JA8E
chains in the Genus database with same CATH superfamily
1DZFA 4A3FE 5IP9E 3H3VF 3GTJE 4XSXE 2KRXA 2VUME 5C4JE 2NVYF 3HOVF 4Q4ZE 4OINE 1TWGF 3EQLE 4JK1E 2NVYE 3S14F 1SMYE 1YNJK 2CW0E 3HOVE 2WAQK 3S1NF 2PPBE 1TWGE 3S14E 2R92F 3S1NE 3HKZH 2JA6F 5FJ8F 4G7HE 1HQME 4Y52F 3H0GF 4A3CE 2JA6E 4XLPE 4BBRF 4G7OE 5M5WE 5FJ8E 2E2HF 4A3BF 4Y52E 4GZYE 3H0GE 1IW7E 3K7AF 4OIRE 4BBRE 3S16F 3S17F 2E2HE 4A3BE 1I6VE 3M4OF 3K7AE 3PO2F 3S17E 3S16E 4LK1E 5IYCF 2A69E 3M4OE 5IP7F 3PO2E 3RZDF 5D4EE 4A3FF 4BY1F 5E18E 3GTJF 5BYHE 5IP7E 3RZDE 4Y7NF 4A93F 2WB1I 5C4JF 4BY1E 2PMZH 1R9TF 1YNNK 3HKZK 4MEYE 4Y7NE 4A93E 5M3FF 4A3KF 1R9TE 1I3QF 4C3IF 4YFNE 1K83F 5M3FE 4A3KE 4QIWH 2A6EE 1I3QE 4C3IE 4A3DF 1K83E 5C44F 1EIKA 1TWCF 5D4DE 1Y1WF 4C2ME 4A3DE 5C44E 4A3ME 4A3CF 1TWCE 1Y1WE 3S2HE 2A6HE 5M5WF 4XLNE 2B63F 3HOXF 3PO3F 4AYBH 5D4CE 1TWAF 4BXXF 2B63E 3HOXE 3PO3E 4KN7E 4YFKE 1TWAE 4BXXE 5C3EE 4ZH4E 4A3LE 4KMUE 4G7ZE 4KN4E 1Y1VF 5FLMF 3GTOF 2NVXF 2NVQF 2E2JF 3S15F 1Y1VE 5FLME 3GTOE 2NVXE 4LLGE 2NVQE 2E2JE 2O5JE 3S1QF 3S15E 3HOZF 3S1RE 3S1QE 3DXJE 3HOWF 4A3GF 3GTKF 3HOZE 1TWFF 4AYBK 2JA5F 4MQ9E 4A3GE 3HOWE 4C2MF 5IYBE 3GTKE 4A3MF 3M3YF 1TWFE 2JA5E 2A68E 3I4MF 3S2HF 3RZOF 2JA7E 2WAQH 2NVTF 4A3IF 4OIPE 3M3YE 3I4ME 3WODE 1SFOE 4OIOE 3RZOE 2NVTE 4A3EF 3S1ME 4BY7F 4A3IE 4MEXE 3GTMF 2Y0SH 3H3VG 3GTQF 3GTGF 4A3EE 3HOUE 3GTME 4BY7E 3GTQE 5C3EF 4Q5SE 1ZYRE 4A3LF 3GTGE 4BBSE 2PMZK 4C3HF 4C3JF 3S2DF 1QKLA 3I4NF 5IYDF 2WB1H 4C3JE 3S2DE 4C3HE 3CQZE 3FKIF 4LK0E 3I4NE 5IYDE 5TMFE 4OIQE 4QIWK 2O5IE 4X6AF 1I6HF 2E2IF 4X6AE 3FKIE 5M5YF 1I6HE 3S1RF 2E2IE 1WCMF 5M5YE 5TMCE 4XSZE 4A3JF 3GTPF 2R7ZF 3GTLF 1WCME 4YG2E 5IYBF 4A3JE 3GTPE 2R7ZE 2YU9F 3GTLE 5C4XF 2JA7F 2R92E 2R93F 2YU9E 5C4XE 1SFOF 3HOYF 5E17E 1I50F 5M5XF 2R93E 3S1MF 3HOYE 3HOUF 1I50E 5M5XE 1TWHF 4YFXE 4BBSF 2Y0SI 5IPLE 5M3MF 1TWHE 2JA8F 3CQZF 5IYCE 5IP9F 5M3ME 2BE5E 2JA8E 2VUMF 4LJZE
chains in the Genus database with same CATH topology
1DZFA 4A3FE 5IP9E 3H3VF 3GTJE 2VUME 5C4JE 2NVYE 3HOVE 1TWGE 3S14E 3S1NE 3HKZH 4A3CE 2JA6E 5M5WE 5FJ8E 4Y52E 3H0GE 4BBRE 2E2HE 4A3BE 3K7AE 3S17E 3S16E 3M4OE 3PO2E 5IP7E 3RZDE 4BY1E 2PMZH 4Y7NE 4A93E 1R9TE 5M3FE 4A3KE 4QIWH 1I3QE 4C3IE 1K83E 1EIKA 4C2ME 4A3DE 5C44E 4A3ME 1TWCE 1Y1WE 3S2HE 4AYBH 2B63E 3HOXE 3PO3E 1TWAE 4BXXE 5C3EE 4A3LE 1Y1VE 5FLME 3GTOE 2NVXE 2NVQE 2E2JE 3S15E 3S1RE 3S1QE 3HOZE 4A3GE 3HOWE 5IYBE 3GTKE 1TWFE 2JA5E 2JA7E 2WAQH 3M3YE 3I4ME 1SFOE 3RZOE 2NVTE 3S1ME 4A3IE 2Y0SH 4A3EE 3HOUE 3GTME 4BY7E 3GTQE 3GTGE 4BBSE 2WB1H 4C3JE 3S2DE 4C3HE 3CQZE 3I4NE 5IYDE 4X6AE 3FKIE 1I6HE 2E2IE 5M5YE 1WCME 4A3JE 3GTPE 2R7ZE 3GTLE 2R92E 2YU9E 5C4XE 2R93E 3HOYE 1I50E 5M5XE 1TWHE 5IYCE 5M3ME 2JA8E
chains in the Genus database with same CATH homology


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