3H3VM

Yeast rnap ii containing poly(a)-signal sequence in the active site
Total Genus 2
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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
2
sequence length
46
structure length
46
Chain Sequence
ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR
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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 Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
molecule tags Transferase/dna/rna
total genus 2
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2009-04-17

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
M PF03604 DNA_RNApol_7kD DNA directed RNA polymerase, 7 kDa subunit
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.20.28.30 Mainly Beta Single Sheet Rubrerythrin, domain 2 RNA polymerase ii, chain L 3h3vM00
1Y1VL 4QIWP 5M3FL 1K83L 3HOXL 4BBRL 5FJ8L 3S15L 3HOUL 2JA7L 4A3LL 3GTML 3GTLL 5C44L 2JA8L 3I4ML 3K7AL 4A93L 3S2HL 3GTJL 3GTOL 2NVYL 2VUML 3I4NL 3S17L 5C4XL 1Y1WL 2R7ZL 4C3IL 3S1ML 2E2JL 4Y52L 3CQZL 3S14L 4A3DL 5IYBL 5M5YL 3S1QL 2B63L 3S1NL 5IYCL 3HOYL 5C3EL 3PO2L 2Y0SP 2WB1P 3RZDL 3M4OL 5C4JL 4AYBP 2NVXL 1TWHL 5M3ML 2WAQP 1I6HL 3GTPL 2JA6L 5IP9L 3GTQL 4A3FL 4A3GL 4BY7L 4A3BL 2R92L 3HKZP 5FLML 4C3JL 1R9TL 3H0GL 3RZOL 5M5WL 3HOWL 3M3YL 4A3JL 1SFOL 4X6AL 1TWGL 2E2HL 3PO3L 5IP7L 4BXXL 1I50L 2PMZP 2E2IL 3S1RL 2NVTL 4Y7NL 4A3IL 4BY1L 1TWAL 1I3QL 3GTKL 3HOVL 2YU9L 2JA5L 1WCML 5IYDL 3FKIL 4A3ML 3H3VM 3HOZL 1TWCL 2NVQL 3S16L 1TWFL 3GTGL 2R93L 3S2DL 4C3HL 4A3EL 4A3KL 4C2M1 4A3CL 4BBSL 5M5XL
chains in the Genus database with same CATH superfamily
1YV1A 1Y1VL 5GADc 1ZRPA 3S15L 4A3LL 1VZGA 1YUZA 1IRNA 3FDJA 1IW7D 5C44L 5MGNA 2JA8L 3K7AL 1QCVA 4A93L 3GTJL 3KYVA 1VZIA 2MS3A 2VUML 5C4XL 3ZG6A 1RDVA 3S1ML 2K2DA 1QQTA 3MPSA 2PYAA 3LNLA 1IU6A 5M5YL 2XJPA 3B0AB 3KYXA 3PZAA 4AI0A 3WWLA 1ODHA 2Y0SP 3VPBE 3H9CA 4AYBP 1TWHL 5JVH1 1YUXA 5IP9L 3NFPI 4A3GL 3MQKB 1BE7A 5DM61 4TPUA 5MFPA 5JVG1 1LTLA 3H99A 2CR8A 3RZOL 1RYTA 3HOWL 4A3JL 2ERJA 2PVXA 1Z92B 1SMWA 4K9FA 1B71A 1S24A 2JI2A 1BQ8A 2M4YA 5GAEc 4UY81 2YU9L 4G6BA 4POFA 3FKIL 1R0IA 1CAAA 5DM71 1TWFL 3GTGL 2A69D 2R93L 3S2DL 4A3EL 2O5JD 1IU5A 2DSXA 2ERSA 4QIWP 4YWLA 4AHZA 1K83L 4BBRL 3GTML 2V3BB 3KYYA 3GTLL 1LKPA 3PKJA 5H1Sc 4V196 4AHWA 3I4NL 3S17L 3PIO1 1BQ9A 1NXGA 5GAHc 3LWOB 4TVMA 3RZ6A 2XJVA 1SMMA 3S14L 4A3DL 2EY4E 1B13A 2V0FA 5EINC 3HAXC 1S30A 3S1QL 3PIP1 3B08B 2PVEA 3IU3I 1H7VA 2B63L 3S1NL 5MF6A 5K2ME 4AR4A 2NYDA 1RB9A 2RFKB 2GMGA 4U671 1F4LA 1T9OA 2WAQP 3GTPL 2JA6L 2XJRA 2CKCA 3GTQL 4LHLA 1QYBA 1PZXA 3HKZP 1LKMA 5EIOC 4JAGA 5AI3A 4C3JL 3QQCE 3H0GL 5M5WL 3M3YL 1SFOL 2KKDA 2E2HL 3PKIA 1I50L 4JAFA 3RYGA 4BY1L 1TWAL 1I3QL 3HJYB 3H3VM 1TWCL 2Z3RB 3S16L 1S2ZA 3HJWB 2CKAA 1WJVA 4AI1A 3K35A 4A3KL 6RXNA 1PFVA 3KYUA 4BBSL 5M5XL 1NXEA 5M3FL 2A6ED 4JADA 4AR6A 2RDVA 5FJ8L 4E6YA 2JA7L 2HR5A 4AI3A 1VZHA 4AI2A 1JYBA 1R0FA 5RXNA 2H12A 2NVYL 1R0HA 2R7ZL 5IY0A 2QL0A 2M6PA 4C3IL 3P8BA 2LCQA 4POGA 4AHXA 5IYBL 5GAGc 2B5ID 1PFUA 2AQCA 1B2OA 2J9UB 3KYWA 3PL5A 5MFZA 1NNQA 5IYCL 3HOYL 5C3EL 1C09A 2WB1P 5C4JL 1T9QA 4WFN1 4RXNA 1LKOA 5M3ML 3J7Y1 3MSUA 4YWMA 5AN9H 4ZN3B 2XJUA 1RYQA 2APOB 4A3BL 2R92L 1RWDA 2C6BA 4AR3A 2VL6A 1R9TL 5AI2A 4AHYA 3WWNB 4B8CD 2AYJA 4X6AL 3LWRB 7RXNA 3PO3L 2XJSA 4BXXL 2PMZP 2E2IL 2NVTL 1VCXA 1DX8A 1YK4A 2KN9A 3H97A 3HOVL 5IYDL 4XXBB 3SS2A 3JR7A 2JI1A 8RXNA 1PFYA 3HOZL 2Z3QB 3PWFA 1IROA 2XJQA 4C2M1 1T9PA 4A3CL 2C6AA 2M4VA 3H9BA 3HOXL 2JI3A 3HOUL 3P2AA 1DVBA 3I4ML 1BFYA 3S2HL 1RDGA 3LWVB 3GTOL 3J7Z1 1Y1WL 1P7PA 1YK5A 4LHNA 2E2JL 1SMUA 2L0ZA 5MLC3 1E8JA 3A44A 4Y52L 3CQZL 2A6HD 1PFWA 2ZIXA 1FHHA 2BE5D 4ME3A 3PO2L 2PSMC 3RZDL 3M4OL 4AR5A 2NVXL 4XGHA 1CADA 1I6HL 2HVYC 2AUSB 4A3FL 3QVDA 4BY7L 2XJTA 1R0GA 5FLML 1R0JA 2PPTA 1TWGL 3LWQB 4GS7D 5IP7L 1BRFA 3S1RL 1FHMA 2A68D 4Y7NL 4A3IL 3GTKL 3LPEB 2M6OA 2JA5L 1OWCA 1WCML 1B2JA 4A3ML 4JAEA 2NVQL 1OWBA 3LWPB 4ZN1B 4C3HL 3RZTA 2V0EA
chains in the Genus database with same CATH topology
1Y1VL 4QIWP 5M3FL 1K83L 3HOXL 4BBRL 5FJ8L 3S15L 3HOUL 2JA7L 4A3LL 3GTML 3GTLL 5C44L 2JA8L 3I4ML 3K7AL 4A93L 3S2HL 3GTJL 3GTOL 2NVYL 2VUML 3I4NL 3S17L 5C4XL 1Y1WL 2R7ZL 4C3IL 3S1ML 2E2JL 4Y52L 3CQZL 3S14L 4A3DL 5IYBL 5M5YL 3S1QL 2B63L 3S1NL 5IYCL 3HOYL 5C3EL 3PO2L 2Y0SP 2WB1P 3RZDL 3M4OL 5C4JL 4AYBP 2NVXL 1TWHL 5M3ML 2WAQP 1I6HL 3GTPL 2JA6L 5IP9L 3GTQL 4A3FL 4A3GL 4BY7L 4A3BL 2R92L 3HKZP 5FLML 4C3JL 1R9TL 3H0GL 3RZOL 5M5WL 3HOWL 3M3YL 4A3JL 1SFOL 4X6AL 1TWGL 2E2HL 3PO3L 5IP7L 4BXXL 1I50L 2PMZP 2E2IL 3S1RL 2NVTL 4Y7NL 4A3IL 4BY1L 1TWAL 1I3QL 3GTKL 3HOVL 2YU9L 2JA5L 1WCML 5IYDL 3FKIL 4A3ML 3H3VM 3HOZL 1TWCL 2NVQL 3S16L 1TWFL 3GTGL 2R93L 3S2DL 4C3HL 4A3EL 4A3KL 4C2M1 4A3CL 4BBSL 5M5XL
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1Y1V L;  4QIW P;  5M3F L;  1K83 L;  3HOX L;  4BBR L;  5FJ8 L;  3S15 L;  3HOU L;  2JA7 L;  4A3L L;  3GTM L;  3GTL L;  5C44 L;  2JA8 L;  3I4M L;  3K7A L;  4A93 L;  3S2H L;  3GTJ L;  3GTO L;  2NVY L;  2VUM L;  3I4N L;  3S17 L;  5C4X L;  1Y1W L;  2R7Z L;  4C3I L;  3S1M L;  2E2J L;  4Y52 L;  3CQZ L;  3S14 L;  4A3D L;  5IYB L;  5M5Y L;  3S1Q L;  2B63 L;  3S1N L;  5IYC L;  3HOY L;  5C3E L;  3PO2 L;  2Y0S P;  2WB1 P;  3RZD L;  3M4O L;  5C4J L;  4AYB P;  2NVX L;  1TWH L;  5M3M L;  2WAQ P;  1I6H L;  3GTP L;  2JA6 L;  5IP9 L;  3GTQ L;  4A3F L;  4A3G L;  4BY7 L;  4A3B L;  2R92 L;  3HKZ P;  5FLM L;  4C3J L;  1R9T L;  3H0G L;  3RZO L;  5M5W L;  3HOW L;  3M3Y L;  4A3J L;  1SFO L;  4X6A L;  1TWG L;  2E2H L;  3PO3 L;  5IP7 L;  4BXX L;  1I50 L;  2PMZ P;  2E2I L;  3S1R L;  2NVT L;  4Y7N L;  4A3I L;  4BY1 L;  1TWA L;  1I3Q L;  3GTK L;  3HOV L;  2YU9 L;  2JA5 L;  1WCM L;  5IYD L;  3FKI L;  4A3M L;  3H3V M;  3HOZ L;  1TWC L;  2NVQ L;  3S16 L;  1TWF L;  3GTG L;  2R93 L;  3S2D L;  4C3H L;  4A3E L;  4A3K L;  4C2M 1;  4A3C L;  4BBS L;  5M5X L; 
#chains in the Genus database with same CATH topology
 1YV1 A;  1Y1V L;  5GAD c;  1ZRP A;  3S15 L;  4A3L L;  1VZG A;  1YUZ A;  1IRN A;  3FDJ A;  1IW7 D;  5C44 L;  5MGN A;  2JA8 L;  3K7A L;  1QCV A;  4A93 L;  3GTJ L;  3KYV A;  1VZI A;  2MS3 A;  2VUM L;  5C4X L;  3ZG6 A;  1RDV A;  3S1M L;  2K2D A;  1QQT A;  3MPS A;  2PYA A;  3LNL A;  1IU6 A;  5M5Y L;  2XJP A;  3B0A B;  3KYX A;  3PZA A;  4AI0 A;  3WWL A;  1ODH A;  2Y0S P;  3VPB E;  3H9C A;  4AYB P;  1TWH L;  5JVH 1;  1YUX A;  5IP9 L;  3NFP I;  4A3G L;  3MQK B;  1BE7 A;  5DM6 1;  4TPU A;  5MFP A;  5JVG 1;  1LTL A;  3H99 A;  2CR8 A;  3RZO L;  1RYT A;  3HOW L;  4A3J L;  2ERJ A;  2PVX A;  1Z92 B;  1SMW A;  4K9F A;  1B71 A;  1S24 A;  2JI2 A;  1BQ8 A;  2M4Y A;  5GAE c;  4UY8 1;  2YU9 L;  4G6B A;  4POF A;  3FKI L;  1R0I A;  1CAA A;  5DM7 1;  1TWF L;  3GTG L;  2A69 D;  2R93 L;  3S2D L;  4A3E L;  2O5J D;  1IU5 A;  2DSX A;  2ERS A;  4QIW P;  4YWL A;  4AHZ A;  1K83 L;  4BBR L;  3GTM L;  2V3B B;  3KYY A;  3GTL L;  1LKP A;  3PKJ A;  5H1S c;  4V19 6;  4AHW A;  3I4N L;  3S17 L;  3PIO 1;  1BQ9 A;  1NXG A;  5GAH c;  3LWO B;  4TVM A;  3RZ6 A;  2XJV A;  1SMM A;  3S14 L;  4A3D L;  2EY4 E;  1B13 A;  2V0F A;  5EIN C;  3HAX C;  1S30 A;  3S1Q L;  3PIP 1;  3B08 B;  2PVE A;  3IU3 I;  1H7V A;  2B63 L;  3S1N L;  5MF6 A;  5K2M E;  4AR4 A;  2NYD A;  1RB9 A;  2RFK B;  2GMG A;  4U67 1;  1F4L A;  1T9O A;  2WAQ P;  3GTP L;  2JA6 L;  2XJR A;  2CKC A;  3GTQ L;  4LHL A;  1QYB A;  1PZX A;  3HKZ P;  1LKM A;  5EIO C;  4JAG A;  5AI3 A;  4C3J L;  3QQC E;  3H0G L;  5M5W L;  3M3Y L;  1SFO L;  2KKD A;  2E2H L;  3PKI A;  1I50 L;  4JAF A;  3RYG A;  4BY1 L;  1TWA L;  1I3Q L;  3HJY B;  3H3V M;  1TWC L;  2Z3R B;  3S16 L;  1S2Z A;  3HJW B;  2CKA A;  1WJV A;  4AI1 A;  3K35 A;  4A3K L;  6RXN A;  1PFV A;  3KYU A;  4BBS L;  5M5X L;  1NXE A;  5M3F L;  2A6E D;  4JAD A;  4AR6 A;  2RDV A;  5FJ8 L;  4E6Y A;  2JA7 L;  2HR5 A;  4AI3 A;  1VZH A;  4AI2 A;  1JYB A;  1R0F A;  5RXN A;  2H12 A;  2NVY L;  1R0H A;  2R7Z L;  5IY0 A;  2QL0 A;  2M6P A;  4C3I L;  3P8B A;  2LCQ A;  4POG A;  4AHX A;  5IYB L;  5GAG c;  2B5I D;  1PFU A;  2AQC A;  1B2O A;  2J9U B;  3KYW A;  3PL5 A;  5MFZ A;  1NNQ A;  5IYC L;  3HOY L;  5C3E L;  1C09 A;  2WB1 P;  5C4J L;  1T9Q A;  4WFN 1;  4RXN A;  1LKO A;  5M3M L;  3J7Y 1;  3MSU A;  4YWM A;  5AN9 H;  4ZN3 B;  2XJU A;  1RYQ A;  2APO B;  4A3B L;  2R92 L;  1RWD A;  2C6B A;  4AR3 A;  2VL6 A;  1R9T L;  5AI2 A;  4AHY A;  3WWN B;  4B8C D;  2AYJ A;  4X6A L;  3LWR B;  7RXN A;  3PO3 L;  2XJS A;  4BXX L;  2PMZ P;  2E2I L;  2NVT L;  1VCX A;  1DX8 A;  1YK4 A;  2KN9 A;  3H97 A;  3HOV L;  5IYD L;  4XXB B;  3SS2 A;  3JR7 A;  2JI1 A;  8RXN A;  1PFY A;  3HOZ L;  2Z3Q B;  3PWF A;  1IRO A;  2XJQ A;  4C2M 1;  1T9P A;  4A3C L;  2C6A A;  2M4V A;  3H9B A;  3HOX L;  2JI3 A;  3HOU L;  3P2A A;  1DVB A;  3I4M L;  1BFY A;  3S2H L;  1RDG A;  3LWV B;  3GTO L;  3J7Z 1;  1Y1W L;  1P7P A;  1YK5 A;  4LHN A;  2E2J L;  1SMU A;  2L0Z A;  5MLC 3;  1E8J A;  3A44 A;  4Y52 L;  3CQZ L;  2A6H D;  1PFW A;  2ZIX A;  1FHH A;  2BE5 D;  4ME3 A;  3PO2 L;  2PSM C;  3RZD L;  3M4O L;  4AR5 A;  2NVX L;  4XGH A;  1CAD A;  1I6H L;  2HVY C;  2AUS B;  4A3F L;  3QVD A;  4BY7 L;  2XJT A;  1R0G A;  5FLM L;  1R0J A;  2PPT A;  1TWG L;  3LWQ B;  4GS7 D;  5IP7 L;  1BRF A;  3S1R L;  1FHM A;  2A68 D;  4Y7N L;  4A3I L;  3GTK L;  3LPE B;  2M6O A;  2JA5 L;  1OWC A;  1WCM L;  1B2J A;  4A3M L;  4JAE A;  2NVQ L;  1OWB A;  3LWP B;  4ZN1 B;  4C3H L;  3RZT A;  2V0E A; 
#chains in the Genus database with same CATH homology
 1Y1V L;  4QIW P;  5M3F L;  1K83 L;  3HOX L;  4BBR L;  5FJ8 L;  3S15 L;  3HOU L;  2JA7 L;  4A3L L;  3GTM L;  3GTL L;  5C44 L;  2JA8 L;  3I4M L;  3K7A L;  4A93 L;  3S2H L;  3GTJ L;  3GTO L;  2NVY L;  2VUM L;  3I4N L;  3S17 L;  5C4X L;  1Y1W L;  2R7Z L;  4C3I L;  3S1M L;  2E2J L;  4Y52 L;  3CQZ L;  3S14 L;  4A3D L;  5IYB L;  5M5Y L;  3S1Q L;  2B63 L;  3S1N L;  5IYC L;  3HOY L;  5C3E L;  3PO2 L;  2Y0S P;  2WB1 P;  3RZD L;  3M4O L;  5C4J L;  4AYB P;  2NVX L;  1TWH L;  5M3M L;  2WAQ P;  1I6H L;  3GTP L;  2JA6 L;  5IP9 L;  3GTQ L;  4A3F L;  4A3G L;  4BY7 L;  4A3B L;  2R92 L;  3HKZ P;  5FLM L;  4C3J L;  1R9T L;  3H0G L;  3RZO L;  5M5W L;  3HOW L;  3M3Y L;  4A3J L;  1SFO L;  4X6A L;  1TWG L;  2E2H L;  3PO3 L;  5IP7 L;  4BXX L;  1I50 L;  2PMZ P;  2E2I L;  3S1R L;  2NVT L;  4Y7N L;  4A3I L;  4BY1 L;  1TWA L;  1I3Q L;  3GTK L;  3HOV L;  2YU9 L;  2JA5 L;  1WCM L;  5IYD L;  3FKI L;  4A3M L;  3H3V M;  3HOZ L;  1TWC L;  2NVQ L;  3S16 L;  1TWF L;  3GTG L;  2R93 L;  3S2D L;  4C3H L;  4A3E L;  4A3K L;  4C2M 1;  4A3C L;  4BBS L;  5M5X L; 
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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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