4Y52E

Crystal structure of 5-carboxycytosine recognition by rna polymerase ii during transcription elongation.
Total Genus 51
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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
51
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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publication title Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
pubmed doi rcsb
molecule tags Transcription/dna/rna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 51
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2015-02-11

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 4y52E01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 4y52E02
2VUME 4BY1E 5C3EE 4A93E 1SFOE 2R92E 5C4XE 3S1ME 2JA8E 3PO3E 3GTQE 3S2HE 5IYBE 2NVYE 1Y1WE 2WB1H 3HOYE 3S1NE 3GTKE 4BBRE 3FKIE 2E2HE 4C2ME 2R93E 1I6HE 5M5YE 3GTPE 3S16E 4BY7E 5IYCE 3I4NE 4BBSE 1R9TE 4A3JE 1WCME 4A3IE 2JA5E 1TWFE 2E2IE 4A3ME 3H0GE 1K83E 5IP9E 1TWCE 3CQZE 4X6AE 3H3VF 1TWGE 3K7AE 5M3FE 3HKZH 4A3KE 1DZFA 4A3EE 3HOVE 3HOXE 4A3FE 4BXXE 3HOWE 5C44E 4A3CE 3HOZE 3RZDE 2PMZH 4Y7NE 5FJ8E 4C3JE 4C3IE 2E2JE 4A3BE 3GTME 2NVXE 5M5XE 4A3DE 4A3LE 2Y0SH 2JA7E 1TWAE 5M3ME 3RZOE 4QIWH 5IP7E 2YU9E 3S14E 1TWHE 3GTOE 4Y52E 4AYBH 2R7ZE 3S1RE 3S2DE 4A3GE 3S1QE 3I4ME 3GTJE 2JA6E 2B63E 2NVTE 1Y1VE 5FLME 5IYDE 4C3HE 3M3YE 1EIKA 2NVQE 3GTGE 5C4JE 3M4OE 3S17E 2WAQH 1I3QE 1I50E 3HOUE 3PO2E 3S15E 3GTLE 5M5WE
chains in the Genus database with same CATH superfamily
2VUME 5IP9F 4BY1E 5C3EE 4A93E 3GTGF 3WODE 1SFOE 2R92E 5C4XE 3S17F 5D4DE 4X6AF 2E2HF 2KRXA 2A69E 3S1ME 5M3FF 3S2HF 2JA8E 3PO3E 3GTQE 2NVYF 3S2HE 3S1MF 4GZYE 3HOXF 5IYBE 4LK1E 2E2IF 2NVYE 1Y1WE 2WB1H 3HOYE 3DXJE 1YNJK 2BE5E 4Q5SE 3S1NE 5IYBF 3GTKE 4XLNE 4BBRE 1IW7E 3GTOF 1Y1VF 5FLMF 1TWGF 3K7AF 4YFXE 4BY7F 3HOZF 3FKIE 4KMUE 2E2HE 4OIPE 3S1RF 1I6HF 3FKIF 5D4CE 4C2ME 4A3JF 2R93E 1I6HE 4A3EF 4MEXE 3H3VG 5E17E 4JK1E 3GTQF 5TMCE 5M5YE 3GTPE 2E2JF 2WAQK 1TWFF 3S16E 1HQME 4YFNE 1I6VE 3I4NF 4BY7E 5IYCE 3I4NE 4BBSE 4LK0E 1R9TE 4A3JE 4YG2E 4C2MF 4C3JF 4C3IF 4YFKE 1WCME 4KN7E 4OIQE 1SMYE 3PO2F 4A3IE 4OIOE 2JA5E 4G7OE 4G7HE 4A3IF 1TWFE 1K83F 5TMFE 2E2IE 4A3ME 3H0GE 4A3DF 2VUMF 1K83E 5IP9E 4G7ZE 1TWCE 4OIRE 3S1NF 2Y0SI 3CQZE 4KN4E 3GTKF 4X6AE 2R92F 3H3VF 1TWGE 3K7AE 1WCMF 2WB1I 4Y52F 2A6EE 5BYHE 5M3FE 3HKZH 4A3KE 4QIWK 1DZFA 4A3EE 3HOVE 2JA5F 3HOXE 4A3FE 3HOYF 4BXXE 2YU9F 4A3FF 3H0GF 2JA6F 3HOWE 5C44E 2PMZK 3CQZF 3S16F 4A3CE 3EQLE 3HOZE 2A68E 5IYDF 3RZDE 2PMZH 5D4EE 4Y7NE 4XSXE 5FJ8E 3HOVF 4C3JE 4C3IE 2E2JE 3GTPF 4A3BE 3GTME 1TWAF 2NVXE 5M5XE 2NVXF 4A3CF 4A3MF 3RZDF 4A3DE 4A3LE 2NVQF 2Y0SH 4Y7NF 2JA7E 1TWAE 3GTMF 4A3GF 5M3ME 3RZOE 4LJZE 2O5JE 4QIWH 3I4MF 3S14F 1YNNK 5IP7E 2B63F 2YU9E 3S14E 1TWCF 1TWHE 1Y1WF 2NVTF 4BXXF 4BY1F 1TWHF 1QKLA 3GTOE 4BBRF 4Y52E 4MEYE 4AYBH 2R7ZE 4C3HF 3M3YF 1ZYRE 2JA7F 2R7ZF 4A3KF 3S1RE 3S2DE 4A3GE 3S1QF 5IPLE 3M4OF 3S1QE 3S2DF 2R93F 5E18E 3I4ME 3GTJE 4LLGE 2JA6E 2B63E 2NVTE 5IP7F 5M5YF 2O5IE 3GTJF 5C44F 2PPBE 3HOWF 4ZH4E 5M5XF 1Y1VE 5FLME 4XSZE 5IYDE 4C3HE 3M3YE 3S15F 1EIKA 3GTLF 4Q4ZE 2A6HE 5IYCF 5C4JF 2NVQE 2CW0E 5FJ8F 3GTGE 5C3EF 4A93F 5C4JE 4A3LF 3M4OE 1R9TF 3S17E 1SFOF 5C4XF 4A3BF 4MQ9E 2WAQH 1I3QE 1I50F 3HOUF 1I50E 3HOUE 3PO2E 1I3QF 5M3MF 3HKZK 4OINE 2JA8F 3RZOF 3PO3F 5M5WF 4AYBK 4XLPE 3S15E 3GTLE 4BBSF 5M5WE
chains in the Genus database with same CATH topology
2VUME 4BY1E 5C3EE 4A93E 1SFOE 2R92E 5C4XE 3S1ME 2JA8E 3PO3E 3GTQE 3S2HE 5IYBE 2NVYE 1Y1WE 2WB1H 3HOYE 3S1NE 3GTKE 4BBRE 3FKIE 2E2HE 4C2ME 2R93E 1I6HE 5M5YE 3GTPE 3S16E 4BY7E 5IYCE 3I4NE 4BBSE 1R9TE 4A3JE 1WCME 4A3IE 2JA5E 1TWFE 2E2IE 4A3ME 3H0GE 1K83E 5IP9E 1TWCE 3CQZE 4X6AE 3H3VF 1TWGE 3K7AE 5M3FE 3HKZH 4A3KE 1DZFA 4A3EE 3HOVE 3HOXE 4A3FE 4BXXE 3HOWE 5C44E 4A3CE 3HOZE 3RZDE 2PMZH 4Y7NE 5FJ8E 4C3JE 4C3IE 2E2JE 4A3BE 3GTME 2NVXE 5M5XE 4A3DE 4A3LE 2Y0SH 2JA7E 1TWAE 5M3ME 3RZOE 4QIWH 5IP7E 2YU9E 3S14E 1TWHE 3GTOE 4Y52E 4AYBH 2R7ZE 3S1RE 3S2DE 4A3GE 3S1QE 3I4ME 3GTJE 2JA6E 2B63E 2NVTE 1Y1VE 5FLME 5IYDE 4C3HE 3M3YE 1EIKA 2NVQE 3GTGE 5C4JE 3M4OE 3S17E 2WAQH 1I3QE 1I50E 3HOUE 3PO2E 3S15E 3GTLE 5M5WE
chains in the Genus database with same CATH homology


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