5C4XF

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
Total Genus 20

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
20
sequence length
87
structure length
87
Chain Sequence
LKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

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
EMPTYTII1 (69-72)TVIII1 (75-78)Updating...
connected with : NaN
molecule tags Transferase/rna/dna
source organism Saccharomyces cerevisiae (strain atcc 204508 / s288c)
publication title Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 20
structure length 87
sequence length 87
ec nomenclature
pdb deposition date 2015-06-18

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
F PF01192 RNA_pol_Rpb6 RNA polymerase Rpb6
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit Eukaryotic RPB6 RNA polymerase subunit 5c4xF00
1R9TF 2O5JE 5E17E 4KMUE 4Q5SE 2NVTF 3RZOF 3GTKF 2WB1I 3GTOF 3S17F 3FKIF 1SMYE 4BY7F 4MEXE 4YFNE 4GZYE 1TWAF 4AYBK 5M5WF 5D4CE 4C3HF 3WODE 1I3QF 2R7ZF 2NVQF 4X6AF 1TWFF 3HOXF 5TMFE 2NVXF 4A3CF 4LK1E 5IPLE 5D4EE 5TMCE 3PO2F 3S15F 1WCMF 4C3IF 1I6HF 2WAQK 3M3YF 4A3IF 1QKLA 2O5IE 5M3FF 1HQME 4ZH4E 2PMZK 2Y0SI 3S1RF 2B63F 5FLMF 3S14F 4LK0E 5C3EF 3GTMF 5M5XF 5E18E 1TWCF 5C44F 4KN7E 4BY1F 5IP7F 5IYBF 4OIPE 3S1MF 4Y52F 4XLPE 3GTLF 2A6EE 1SFOF 2PPBE 4A3BF 3S1NF 3DXJE 3S16F 4BXXF 3HOZF 1Y1VF 4BBRF 2CW0E 3GTGF 4LJZE 4YFXE 4A3KF 3I4NF 5IYDF 5IP9F 3S2HF 4A3EF 3H0GF 4A3LF 5IYCF 3RZDF 3H3VG 3S1QF 3K7AF 3CQZF 3HOVF 4C2MF 3PO3F 4G7OE 4A93F 4MQ9E 4XSXE 2YU9F 4Q4ZE 3I4MF 4Y7NF 1I50F 4XLNE 4G7HE 4A3FF 2JA5F 4YFKE 1ZYRE 2JA7F 2E2HF 2NVYF 4A3JF 3M4OF 2A68E 1IW7E 4MEYE 3S2DF 5C4XF 3GTJF 2A6HE 2BE5E 3GTQF 2R93F 4OIRE 3EQLE 1I6VE 5C4JF 4JK1E 4YG2E 4KN4E 4OIOE 4BBSF 2JA8F 2A69E 1Y1WF 1K83F 3HOUF 4G7ZE 3GTPF 1YNJK 3HKZK 1TWHF 1TWGF 4LLGE 4A3DF 1YNNK 4A3MF 2JA6F 4OINE 4A3GF 2E2JF 5D4DE 4XSZE 3HOWF 2E2IF 5FJ8F 5M3MF 2VUMF 4OIQE 2R92F 4C3JF 5M5YF 3HOYF 5BYHE
chains in the Genus database with same CATH superfamily
1R9TF 2O5JE 5E17E 4KMUE 4Q5SE 4BBSE 2JA8E 2NVTF 3RZOF 1Y1WE 3GTKF 2WB1I 3GTOF 1K83E 3S17F 3HOUE 3GTPE 3FKIF 1SMYE 1TWHE 1TWGE 4BY7F 4A3DE 4MEXE 4A3ME 2JA6E 4YFNE 4GZYE 1TWAF 4A3GE 4AYBK 5M5WF 5D4CE 2E2JE 4C3HF 3HOWE 3WODE 2E2IE 1I3QF 2R7ZF 5FJ8E 2NVQF 4X6AF 1TWFF 3HOXF 5TMFE 5M3ME 2VUME 2R92E 2NVXF 4A3CF 4LK1E 5M5YE 5IPLE 5D4EE 5TMCE 3PO2F 3S15F 1WCMF 4C3IF 1I6HF 2WAQK 3HOYE 3M3YF 4A3IF 1QKLA 1R9TE 2O5IE 5M3FF 1HQME 4ZH4E 2PMZK 2Y0SI 2NVTE 1DZFA 3H3VF 3RZOE 3GTKE 3S1RF 2B63F 5FLMF 3GTOE 3S14F 3S17E 3FKIE 4LK0E 5C3EF 3GTMF 5M5XF 5E18E 4BY7E 1TWCF 5C44F 4KN7E 4BY1F 5IP7F 5IYBF 1TWAE 4OIPE 5M5WE 4Y52F 3S1MF 4C3HE 4XLPE 1I3QE 2R7ZE 3GTLF 2A6EE 1SFOF 2PPBE 1TWFE 2NVQE 3HOXE 4A3BF 3DXJE 3S16F 3S1NF 4BXXF 3HOZF 1Y1VF 4BBRF 2CW0E 3GTGF 4LJZE 2NVXE 4A3CE 4YFXE 4A3KF 3I4NF 2KRXA 4C3JE 5IYDF 5IP9F 3S2HF 4A3EF 3H0GF 3PO2E 3S15E 1WCME 4C3IE 4A3LF 1I6HE 5IYCF 3RZDF 3H3VG 4QIWH 3HKZH 3M3YE 3S1QF 4A3IE 3K7AF 3CQZF 5M3FE 3HOVF 2WB1H 4C2MF 3PO3F 4G7OE 4A93F 3S1RE 2B63E 5FLME 3S14E 5C3EE 4MQ9E 3GTME 4XSXE 5M5XE 2YU9F 4Q4ZE 1EIKA 1TWCE 5C44E 3I4MF 4BY1E 5IYBE 5IP7E 4Y7NF 1I50F 4XLNE 4G7HE 4A3FF 2JA5F 3S1ME 4YFKE 1ZYRE 2JA7F 4Y52E 2E2HF 2NVYF 4A3JF 1SFOE 3GTLE 4A3BE 3S1NE 3M4OF 3S16E 4BXXE 2A68E 1IW7E 1Y1VE 4MEYE 4BBRE 3GTJF 3GTGE 3S2DF 3HOZE 5C4XF 2A6HE 2BE5E 4A3KE 3I4NE 3GTQF 4X6AE 2R93F 5IYDE 5IP9E 3S2HE 4OIRE 3EQLE 1I6VE 3H0GE 5C4JF 4A3EE 4A3LE 5IYCE 3RZDE 4JK1E 4YG2E 2Y0SH 3K7AE 4KN4E 4OIOE 3CQZE 3S1QE 3HOVE 4BBSF 4C2ME 2JA8F 2A69E 3PO3E 1Y1WF 4A93E 4AYBH 1K83F 3HOUF 4G7ZE 3GTPF 1YNJK 4QIWK 3HKZK 1TWHF 2YU9E 1TWGF 4LLGE 4A3DF 1YNNK 4A3MF 2JA6F 4OINE 3I4ME 4A3GF 4Y7NE 1I50E 4A3FE 2JA5E 2JA7E 2E2JF 5D4DE 4XSZE 3HOWF 2E2IF 5FJ8F 2NVYE 4A3JE 2E2HE 3M4OE 5C4XE 3S2DE 5M3MF 3GTJE 2WAQH 4OIQE 2R92F 2VUMF 4C3JF 5M5YF 3GTQE 2PMZH 2R93E 5C4JE 3HOYF 5BYHE
chains in the Genus database with same CATH topology
1R9TF 2O5JE 5E17E 4KMUE 4Q5SE 2NVTF 3RZOF 3GTKF 2WB1I 3GTOF 3S17F 3FKIF 1SMYE 4BY7F 4MEXE 4YFNE 4GZYE 1TWAF 4AYBK 5M5WF 5D4CE 4C3HF 3WODE 1I3QF 2R7ZF 2NVQF 4X6AF 1TWFF 3HOXF 5TMFE 2NVXF 4A3CF 4LK1E 5IPLE 5D4EE 5TMCE 3PO2F 3S15F 1WCMF 4C3IF 1I6HF 2WAQK 3M3YF 4A3IF 1QKLA 2O5IE 5M3FF 1HQME 4ZH4E 2PMZK 2Y0SI 3S1RF 2B63F 5FLMF 3S14F 4LK0E 5C3EF 3GTMF 5M5XF 5E18E 1TWCF 5C44F 4KN7E 4BY1F 5IP7F 5IYBF 4OIPE 3S1MF 4Y52F 4XLPE 3GTLF 2A6EE 1SFOF 2PPBE 4A3BF 3S1NF 3DXJE 3S16F 4BXXF 3HOZF 1Y1VF 4BBRF 2CW0E 3GTGF 4LJZE 4YFXE 4A3KF 3I4NF 2KRXA 5IYDF 5IP9F 3S2HF 4A3EF 3H0GF 4A3LF 5IYCF 3RZDF 3H3VG 3S1QF 3K7AF 3CQZF 3HOVF 4C2MF 3PO3F 4G7OE 4A93F 4MQ9E 4XSXE 2YU9F 4Q4ZE 3I4MF 4Y7NF 1I50F 4XLNE 4G7HE 4A3FF 2JA5F 4YFKE 1ZYRE 2JA7F 2E2HF 2NVYF 4A3JF 3M4OF 2A68E 1IW7E 4MEYE 3S2DF 5C4XF 3GTJF 2A6HE 2BE5E 3GTQF 2R93F 4OIRE 3EQLE 1I6VE 5C4JF 4JK1E 4YG2E 4KN4E 4OIOE 4BBSF 2JA8F 2A69E 1Y1WF 1K83F 3HOUF 4G7ZE 3GTPF 1YNJK 4QIWK 3HKZK 1TWHF 1TWGF 4LLGE 4A3DF 1YNNK 4A3MF 2JA6F 4OINE 4A3GF 2E2JF 5D4DE 4XSZE 3HOWF 2E2IF 5FJ8F 5M3MF 2VUMF 4OIQE 2R92F 4C3JF 5M5YF 3HOYF 5BYHE
chains in the Genus database with same CATH homology


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