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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molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro
pubmed doi rcsb
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
4A3KL 3I4NL 2E2HL 2B63L 4BXXL 4C3IL 4C3JL 1TWAL 3HOYL 3S1QL 1TWHL 3H0GL 5IP7L 2NVYL 3M3YL 3S1ML 1WCML 3GTML 2JA5L 3GTPL 3M4OL 4A3ML 2R7ZL 4BY1L 3GTQL 1TWFL 2YU9L 4QIWP 3GTKL 4A93L 5IYCL 5IYDL 3RZDL 3S2DL 1TWCL 2JA6L 2VUML 2Y0SP 2NVXL 1I3QL 3GTLL 4A3CL 4C3HL 3RZOL 5FJ8L 2R93L 3HKZP 5IP9L 4BBRL 3S2HL 2JA8L 1Y1WL 4AYBP 3CQZL 3PO2L 5M5XL 3K7AL 5FLML 2NVQL 1SFOL 5M5YL 2E2IL 3PO3L 5C44L 2E2JL 3S15L 2WAQP 5IYBL 3GTOL 1R9TL 4A3LL 4BBSL 2WB1P 4Y52L 3S1RL 3HOUL 3H3VM 4X6AL 4A3IL 5M3ML 3HOVL 4C2M1 5M5WL 4Y7NL 3GTJL 3HOZL 5C3EL 1TWGL 4A3EL 4BY7L 2NVTL 4A3GL 1I50L 5C4XL 1I6HL 1Y1VL 3I4ML 3S1NL 2R92L 5M3FL 3HOWL 3S17L 2JA7L 5C4JL 3HOXL 3FKIL 1K83L 3GTGL 4A3JL 4A3BL 3S16L 3S14L 4A3DL 2PMZP 4A3FL
chains in the Genus database with same CATH superfamily
3H97A 1B2OA 2E2HL 4AI0A 4BXXL 4C3IL 3LWRB 1TWAL 3QVDA 6RXNA 5IP7L 3SS2A 1R0IA 3M3YL 2A6ED 2JI2A 1CADA 4BY1L 3GTQL 4YWMA 2YU9L 4QIWP 4A93L 7RXNA 4ME3A 3HJYB 3J7Y1 1R0GA 1BQ8A 3GTLL 1I3QL 3RYGA 3HAXC 4U671 3RZOL 1ZRPA 2PPTA 5MFZA 1SMWA 3ZG6A 1IROA 4XGHA 1DVBA 3B0AB 2CKCA 3K7AL 3PWFA 1BRFA 1DX8A 3PO3L 5C44L 2E2JL 4E6YA 3GTOL 3KYYA 3RZTA 4A3IL 2XJSA 4C2M1 1R0JA 2Z3RB 1YK5A 4RXNA 3VPBE 4A3EL 4AI1A 2NVTL 1RYTA 1VZIA 1H7VA 1RWDA 3PKJA 1R0HA 2M6PA 2GMGA 3GTGL 4A3BL 4A3JL 4K9FA 5MFPA 1PZXA 1T9QA 4A3KL 3P2AA 3I4NL 3LNLA 2O5JD 2AYJA 3HJWB 2LCQA 4C3JL 4ZN3B 1ODHA 1TWHL 3H0GL 1S30A 1WCML 1JYBA 2M6OA 3PZAA 1BFYA 1TWFL 3P8BA 5IYDL 5GAEc 1YK4A 4JADA 1RDGA 3RZDL 3LWOB 1TWCL 3KYUA 2JA6L 5RXNA 2HVYC 2ERJA 4JAFA 1YUZA 8RXNA 2R93L 1PFUA 2DSXA 3HKZP 1FHMA 1NNQA 5JVH1 2RDVA 2V3BB 5AI2A 1B13A 3IU3I 4AYBP 5MGNA 3CQZL 2A6HD 2M4YA 4JAEA 1OWCA 2HR5A 3H9CA 3WWNB 2NVQL 4UY81 3S15L 5IYBL 3LPEB 4A3LL 4LHNA 4BBSL 1NXEA 1C09A 4Y52L 1P7PA 3MQKB 3HOUL 1RDVA 5K2ME 2JI3A 4LHLA 3KYXA 3MSUA 4Y7NL 3GTJL 3HOZL 5C3EL 2XJQA 1TWGL 5DM61 3PKIA 2VL6A 5C4XL 1LKOA 1Y1VL 2PYAA 3I4ML 5MF6A 1VCXA 1Z92B 2M4VA 3JR7A 3LWQB 2R92L 1B71A 3FDJA 2JA7L 1IRNA 4YWLA 5C4JL 3HOXL 1K83L 5DM71 4AHWA 3H99A 1B2JA 4V196 5GADc 2XJVA 3KYVA 1BE7A 4AI3A 1WJVA 3HOYL 3S1QL 3S1ML 2PVXA 1LTLA 3GTML 4AR4A 4A3ML 2R7ZL 1FHHA 1PFVA 2ERSA 3GTKL 5IYCL 2V0EA 3S2DL 3RZ6A 4TVMA 2Y0SP 2NVXL 3K35A 4C3HL 4AI2A 4AR5A 5FJ8L 2V0FA 3PL5A 5IP9L 5GAGc 3PO2L 1RB9A 2KN9A 2APOB 2H12A 1SFOL 5M5YL 2XJRA 2WAQP 5JVG1 1SMUA 5H1Sc 2WB1P 3H3VM 2PSMC 1T9PA 5M3ML 5IY0A 3HOVL 4XXBB 2C6BA 1NXGA 1I50L 2AQCA 5EIOC 1CAAA 3HOWL 1VZHA 3MPSA 1PFWA 3S16L 3S14L 2PVEA 4A3DL 2PMZP 1LKPA 3PIO1 1T9OA 3LWPB 2RFKB 2B63L 3H9BA 4GS7D 5MLC3 1IW7D 2QL0A 2MS3A 3J7Z1 1IU6A 2NVYL 4AR6A 2CR8A 3PIP1 3LWVB 2JA5L 3GTPL 3M4OL 2ZIXA 4TPUA 4AHYA 5AN9H 3NFPI 2AUSB 1S24A 1QQTA 1PFYA 2XJPA 4B8CD 2BE5D 2L0ZA 1OWBA 2VUML 1QYBA 2KKDA 4A3CL 1QCVA 2J9UB 2XJTA 3WWLA 4ZN1B 2A69D 5AI3A 4AR3A 2A68D 1YUXA 2XJUA 4BBRL 4AHXA 3S2HL 2JA8L 1Y1WL 1S2ZA 1IU5A 1BQ9A 4G6BA 1SMMA 4POGA 5M5XL 2C6AA 5GAHc 3A44A 4WFN1 4POFA 5FLML 2E2IL 1R0FA 1R9TL 3KYWA 2EY4E 1E8JA 4AHZA 3S1RL 4X6AL 2K2DA 5M5WL 2NYDA 4BY7L 4A3GL 1I6HL 1VZGA 2Z3QB 2JI1A 3S1NL 3QQCE 5M3FL 1YV1A 2CKAA 3S17L 4JAGA 1LKMA 3FKIL 5EINC 3B08B 1F4LA 1RYQA 2B5ID 4A3FL
chains in the Genus database with same CATH topology
4A3KL 3I4NL 2E2HL 2B63L 4BXXL 4C3IL 4C3JL 1TWAL 3HOYL 3S1QL 1TWHL 3H0GL 5IP7L 2NVYL 3M3YL 3S1ML 1WCML 3GTML 2JA5L 3GTPL 3M4OL 4A3ML 2R7ZL 4BY1L 3GTQL 1TWFL 2YU9L 4QIWP 3GTKL 4A93L 5IYCL 5IYDL 3RZDL 3S2DL 1TWCL 2JA6L 2VUML 2Y0SP 2NVXL 1I3QL 3GTLL 4A3CL 4C3HL 3RZOL 5FJ8L 2R93L 3HKZP 5IP9L 4BBRL 3S2HL 2JA8L 1Y1WL 4AYBP 3CQZL 3PO2L 5M5XL 3K7AL 5FLML 2NVQL 1SFOL 5M5YL 2E2IL 3PO3L 5C44L 2E2JL 3S15L 2WAQP 5IYBL 3GTOL 1R9TL 4A3LL 4BBSL 2WB1P 4Y52L 3S1RL 3HOUL 3H3VM 4X6AL 4A3IL 5M3ML 3HOVL 4C2M1 5M5WL 4Y7NL 3GTJL 3HOZL 5C3EL 1TWGL 4A3EL 4BY7L 2NVTL 4A3GL 1I50L 5C4XL 1I6HL 1Y1VL 3I4ML 3S1NL 2R92L 5M3FL 3HOWL 3S17L 2JA7L 5C4JL 3HOXL 3FKIL 1K83L 3GTGL 4A3JL 4A3BL 3S16L 3S14L 4A3DL 2PMZP 4A3FL
chains in the Genus database with same CATH homology


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