4BBSE

Structure of an initially transcribing rna polymerase ii-tfiib complex
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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publication title Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex
pubmed doi rcsb
source organism Saccharomyces cerevisiae
molecule tags Transcription
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
total genus 60
structure length 214
sequence length 214
ec nomenclature
pdb deposition date 2012-09-27

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 4bbsE01
3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunit 4bbsE02
3S15E 3GTPE 4BXXE 3GTOE 2JA7E 3S1NE 4C3IE 2R92E 1WCME 3HOWE 4A3DE 3K7AE 2JA6E 2Y0SH 5IYDE 3S2HE 5C3EE 1Y1VE 1SFOE 3HOVE 1TWCE 1I3QE 2R7ZE 4A3BE 5C44E 2E2HE 5M5XE 3I4ME 5M5YE 3HOYE 5FLME 3GTME 3HOUE 1I50E 3PO2E 1K83E 4A3FE 3HOZE 4A93E 3H0GE 5IP9E 1Y1WE 4Y52E 4Y7NE 5C4XE 1R9TE 3S14E 2R93E 3S17E 4C3HE 3M4OE 4BBRE 3S16E 4AYBH 4A3ME 2E2JE 5C4JE 5IP7E 4A3GE 2PMZH 4BY1E 4A3IE 2NVXE 3S1QE 4BBSE 2JA5E 1TWHE 3CQZE 2NVTE 4C2ME 5FJ8E 3RZOE 5IYCE 3FKIE 5M3FE 3S2DE 3S1ME 5M3ME 2NVQE 2YU9E 4A3JE 4A3EE 2WB1H 3GTQE 2JA8E 4A3LE 3GTJE 1TWAE 2B63E 2VUME 1DZFA 1TWGE 4C3JE 3M3YE 3GTGE 1TWFE 1EIKA 3I4NE 4A3KE 3S1RE 1I6HE 4X6AE 3PO3E 3HOXE 3GTKE 3H3VF 2WAQH 3GTLE 4BY7E 2NVYE 3RZDE 3HKZH 5IYBE 4A3CE 4QIWH 5M5WE 2E2IE
chains in the Genus database with same CATH superfamily
3S15E 5IYCF 3GTPE 4BXXE 3GTOE 2B63F 2JA7E 1HQME 3S1NE 5FLMF 2NVTF 2O5JE 2A69E 4A3LF 2Y0SI 4C3IE 2R92E 2PPBE 1ZYRE 5IP9F 1WCME 3HOWE 4A3DE 4A3KF 5C44F 2E2HF 3K7AE 2JA6E 1K83F 5M3MF 3CQZF 2R7ZF 2PMZK 1IW7E 1I6VE 4A3IF 2WAQK 2Y0SH 3FKIF 5IYDE 4C3HF 3S2DF 3HOXF 3S2HE 5C3EE 2WB1I 1Y1VE 4LK1E 1SFOE 3HOVE 5C3EF 4A3MF 2E2JF 1YNJK 1TWCE 1I3QE 2A6EE 2R7ZE 4OIOE 4Y7NF 4A3BE 4YFXE 5E18E 4A3BF 5C44E 2E2HE 5M5XE 4Q4ZE 1TWGF 3I4ME 4LJZE 4QIWK 2YU9F 2JA5F 3PO2F 5M5YE 2O5IE 4A93F 3S1MF 3HOYE 4OIPE 4XLPE 2JA8F 5FLME 3GTME 3HOUE 3M4OF 1I50E 3PO2E 1K83E 4A3FE 3HOZE 4A93E 4JK1E 4YFKE 3H0GE 4A3JF 5IP9E 4YG2E 1Y1WE 4Y52E 4Y7NE 1I50F 4KN4E 5C4XE 3WODE 3GTMF 3HOUF 4C3IF 3HOZF 1TWHF 2CW0E 4XSXE 1TWCF 5D4EE 1R9TE 3S14E 4YFNE 2R93E 3H0GF 3RZOF 5FJ8F 5M5YF 3S1QF 3S17E 3S17F 4C3HE 5IYDF 3M4OE 4BBRE 3S16E 2NVXF 3GTPF 1R9TF 4Q5SE 3S14F 4G7OE 3GTLF 3H3VG 4MQ9E 4XLNE 2BE5E 4Y52F 1Y1WF 4A3CF 4AYBH 3PO3F 4A3ME 5M5XF 2E2JE 5C4JE 5IP7E 4A3GE 2PMZH 4G7HE 4BY1E 4LLGE 4A3FF 4BBSF 4A3IE 2A6HE 1YNNK 2NVXE 4LK0E 4BBRF 3HOYF 4KN7E 3S1QE 4BBSE 1SMYE 4A3GF 5C4XF 2JA5E 1QKLA 1TWHE 5D4DE 3CQZE 3I4NF 3GTKF 3GTQF 2NVTE 4C2ME 1TWFF 3S16F 5BYHE 2A68E 1SFOF 3HOVF 2KRXA 4BXXF 4A3EF 3HKZK 5FJ8E 3RZOE 5IYCE 3S15F 5IPLE 3FKIE 5M3FE 3S2DE 4XSZE 3GTJF 3S1ME 5D4CE 5M3ME 2NVQE 5TMCE 5M5WF 4G7ZE 2JA6F 2YU9E 4A3JE 3I4MF 4A3EE 2WB1H 3HOWF 3S1RF 1I6HF 4KMUE 3GTQE 2JA8E 4A3LE 3GTGF 4OINE 4BY7F 3GTJE 1TWAE 2JA7F 2B63E 5TMFE 5E17E 2VUME 1DZFA 1TWGE 4C3JE 3M3YE 3GTGE 1TWFE 4AYBK 3S2HF 1EIKA 1I3QF 3I4NE 4A3KE 1WCMF 4A3DF 5IP7F 3S1RE 1I6HE 4X6AE 5C4JF 1Y1VF 4X6AF 3PO3E 3HOXE 3GTKE 3H3VF 4MEXE 5IYBF 2WAQH 1TWAF 4OIQE 3GTLE 4BY7E 2NVYF 2NVYE 3RZDE 4MEYE 5M3FF 3RZDF 3GTOF 3K7AF 3HKZH 4GZYE 2VUMF 5IYBE 4BY1F 4C2MF 2E2IF 3EQLE 4OIRE 2R93F 2R92F 4A3CE 3DXJE 4ZH4E 4QIWH 5M5WE 2NVQF 3S1NF 3M3YF 2E2IE 4C3JF
chains in the Genus database with same CATH topology
3S15E 3GTPE 4BXXE 3GTOE 2JA7E 3S1NE 4C3IE 2R92E 1WCME 3HOWE 4A3DE 3K7AE 2JA6E 2Y0SH 5IYDE 3S2HE 5C3EE 1Y1VE 1SFOE 3HOVE 1TWCE 1I3QE 2R7ZE 4A3BE 5C44E 2E2HE 5M5XE 3I4ME 5M5YE 3HOYE 5FLME 3GTME 3HOUE 1I50E 3PO2E 1K83E 4A3FE 3HOZE 4A93E 3H0GE 5IP9E 1Y1WE 4Y52E 4Y7NE 5C4XE 1R9TE 3S14E 2R93E 3S17E 4C3HE 3M4OE 4BBRE 3S16E 4AYBH 4A3ME 2E2JE 5C4JE 5IP7E 4A3GE 2PMZH 4BY1E 4A3IE 2NVXE 3S1QE 4BBSE 2JA5E 1TWHE 3CQZE 2NVTE 4C2ME 5FJ8E 3RZOE 5IYCE 3FKIE 5M3FE 3S2DE 3S1ME 5M3ME 2NVQE 2YU9E 4A3JE 4A3EE 2WB1H 3GTQE 2JA8E 4A3LE 3GTJE 1TWAE 2B63E 2VUME 1DZFA 1TWGE 4C3JE 3M3YE 3GTGE 1TWFE 1EIKA 3I4NE 4A3KE 3S1RE 1I6HE 4X6AE 3PO3E 3HOXE 3GTKE 3H3VF 2WAQH 3GTLE 4BY7E 2NVYE 3RZDE 3HKZH 5IYBE 4A3CE 4QIWH 5M5WE 2E2IE
chains in the Genus database with same CATH homology


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