4Y7NE

The structure insight into 5-carboxycytosine recognition by rna polymerase ii during transcription elongation.
Total Genus 53
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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
53
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/dna/rna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
pubmed doi rcsb
total genus 53
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2015-02-15

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 4y7nE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 4y7nE02
4Y52E 3HOXE 4A3IE 4BBRE 1TWGE 4BXXE 5M5WE 1TWCE 3S15E 2NVXE 3PO3E 4A3FE 4QIWH 4X6AE 4C3JE 2R93E 4C3HE 3HOUE 2JA7E 2E2HE 3S16E 4BY1E 3GTJE 2JA5E 1Y1VE 5IP7E 5IYDE 4AYBH 1EIKA 3HOVE 2R7ZE 3GTME 2E2JE 5C4XE 4A3JE 4C2ME 1TWHE 1WCME 3S1NE 5M3FE 2VUME 2YU9E 3GTKE 5M3ME 3FKIE 5FLME 3S1RE 5IYCE 3S1QE 3GTLE 3GTOE 3S14E 4BY7E 1K83E 1I50E 4A3CE 4C3IE 5IP9E 4Y7NE 2PMZH 4A3ME 3HOYE 3HOWE 1I6HE 3GTQE 3S2HE 3PO2E 2R92E 2Y0SH 5C4JE 4A3DE 3I4ME 4BBSE 2WB1H 3H0GE 5FJ8E 1R9TE 3HKZH 3S17E 2WAQH 4A3EE 2E2IE 2B63E 5C44E 3GTPE 2NVTE 3K7AE 5M5YE 1I3QE 4A3BE 3H3VF 5M5XE 3M4OE 3I4NE 1DZFA 4A3LE 2JA8E 5C3EE 1TWFE 3S2DE 3CQZE 3GTGE 4A93E 3HOZE 1TWAE 1Y1WE 4A3KE 3S1ME 3RZDE 3M3YE 2NVYE 3RZOE 4A3GE 5IYBE 2JA6E 2NVQE 1SFOE
chains in the Genus database with same CATH superfamily
4Y52E 3HOXE 4A3IE 1YNJK 5M3FF 2O5IE 3S1NF 4BBRE 4LK1E 1TWGE 2O5JE 4BXXE 5M5WE 1TWCE 3S15E 2NVXE 3PO3E 2YU9F 2VUMF 3GTKF 5M3MF 3FKIF 4A3FE 4MQ9E 4QIWH 5FLMF 3S1RF 5BYHE 5IYCF 4X6AE 4XLNE 4C3JE 3S1QF 2R93E 4G7OE 4C3HE 3HOUE 3GTLF 3GTOF 2JA7E 2E2HE 3S16E 4BY1E 3GTJE 2JA5E 1Y1VE 5IP7E 4BY7F 5IYDE 4LLGE 4AYBH 3S14F 1K83F 1I50F 2WB1I 4A3CF 4OIPE 4C3IF 5IP9F 1EIKA 4Y7NF 3HOVE 4QIWK 2R7ZE 4KN4E 3GTME 4A3MF 2E2JE 5C4XE 4A3JE 4LJZE 1IW7E 3HOYF 3HOWF 4C2ME 4Q5SE 1TWHE 3GTQF 1WCME 3S2HF 3PO2F 2R92F 4JK1E 1I6VE 4XSZE 3WODE 3S1NE 5M3FE 4AYBK 5C4JF 4A3DF 2CW0E 3I4MF 4BBSF 4G7ZE 2KRXA 3H0GF 2VUME 2YU9E 5FJ8F 3GTKE 1R9TF 5M3ME 3FKIE 5FLME 3S1RE 5E18E 4ZH4E 1QKLA 3S17F 4A3EF 5IYCE 2E2IF 5IPLE 3S1QE 2B63F 5TMFE 5C44F 3GTPF 2NVTF 3GTLE 3K7AF 4YFXE 1I3QF 4MEYE 5M5YF 4A3BF 3GTOE 3DXJE 3M4OF 5M5XF 2BE5E 3HOXF 3I4NF 4A3LF 3S14E 4BY7E 2JA8F 4LK0E 3EQLE 1K83E 1I50E 4A3CE 4XSXE 5C3EF 4C3IE 1TWFF 5IP9E 2NVXF 4Y7NE 2PMZH 3S2DF 4A3ME 3CQZF 3HOYE 3HOWE 1I6HE 3GTQE 3GTGF 3S2HE 4MEXE 3PO2E 4A93F 2R92E 3HOZF 1TWAF 1Y1WF 4YFKE 4A3KF 4OIRE 3S1MF 2JA5F 3RZDF 3M3YF 2NVYF 2Y0SH 3RZOF 5C4JE 4A3DE 3I4ME 4A3GF 4BBSE 2PMZK 2WB1H 3H0GE 5FJ8E 1R9TE 5IYBF 2JA6F 5D4CE 3HKZH 2NVQF 3S17E 2WAQH 1SFOF 4A3EE 2E2IE 2B63E 2A68E 5C44E 1HQME 3GTPE 2NVTE 4GZYE 3K7AE 4Y52F 5M5YE 1I3QE 4A3BE 4YFNE 4A3IF 4OIOE 3H3VF 5M5XE 3M4OE 4BBRF 5E17E 4XLPE 1TWGF 3I4NE 4G7HE 4Q4ZE 1TWCF 5M5WF 1DZFA 4A3LE 3S15F 2JA8E 3PO3F 4BXXF 4OINE 4A3FF 5C3EE 1TWFE 3S2DE 2A6HE 4KMUE 3HKZK 1YNNK 2WAQK 3CQZE 4C3JF 4X6AF 2R93F 4OIQE 4C3HF 3HOUF 5D4DE 1ZYRE 1SMYE 3GTGE 2E2HF 4BY1F 2PPBE 2JA7F 5TMCE 3S16F 4A93E 3GTJF 3HOZE 1TWAE 1Y1WE 1Y1VF 4YG2E 4A3KE 5IP7F 5IYDF 3H3VG 3S1ME 3RZDE 3M3YE 2Y0SI 2NVYE 3RZOE 2A69E 4A3GE 3HOVF 2R7ZF 2A6EE 3GTMF 2E2JF 5IYBE 2JA6E 4A3JF 5C4XF 4C2MF 2NVQE 1TWHF 1WCMF 1SFOE 4KN7E 1I6HF 5D4EE
chains in the Genus database with same CATH topology
4Y52E 3HOXE 4A3IE 4BBRE 1TWGE 4BXXE 5M5WE 1TWCE 3S15E 2NVXE 3PO3E 4A3FE 4QIWH 4X6AE 4C3JE 2R93E 4C3HE 3HOUE 2JA7E 2E2HE 3S16E 4BY1E 3GTJE 2JA5E 1Y1VE 5IP7E 5IYDE 4AYBH 1EIKA 3HOVE 2R7ZE 3GTME 2E2JE 5C4XE 4A3JE 4C2ME 1TWHE 1WCME 3S1NE 5M3FE 2VUME 2YU9E 3GTKE 5M3ME 3FKIE 5FLME 3S1RE 5IYCE 3S1QE 3GTLE 3GTOE 3S14E 4BY7E 1K83E 1I50E 4A3CE 4C3IE 5IP9E 4Y7NE 2PMZH 4A3ME 3HOYE 3HOWE 1I6HE 3GTQE 3S2HE 3PO2E 2R92E 2Y0SH 5C4JE 4A3DE 3I4ME 4BBSE 2WB1H 3H0GE 5FJ8E 1R9TE 3HKZH 3S17E 2WAQH 4A3EE 2E2IE 2B63E 5C44E 3GTPE 2NVTE 3K7AE 5M5YE 1I3QE 4A3BE 3H3VF 5M5XE 3M4OE 3I4NE 1DZFA 4A3LE 2JA8E 5C3EE 1TWFE 3S2DE 3CQZE 3GTGE 4A93E 3HOZE 1TWAE 1Y1WE 4A3KE 3S1ME 3RZDE 3M3YE 2NVYE 3RZOE 4A3GE 5IYBE 2JA6E 2NVQE 1SFOE
chains in the Genus database with same CATH homology


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