3HOWL

Complete rna polymerase ii elongation complex iii with a t-u mismatch and a frayed rna 3'-uridine
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
44
structure length
44
Chain Sequence
LKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR
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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 Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
pubmed doi rcsb
molecule tags Transcription,transferase/dna/rna hybrid
total genus 2
structure length 44
sequence length 44
ec nomenclature
pdb deposition date 2009-06-03

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
L 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 3howL00
3S1RL 2B63L 3H3VM 5C4XL 1TWGL 3K7AL 3FKIL 1TWHL 2R7ZL 2Y0SP 2NVXL 5M3ML 3I4ML 4A3FL 1I6HL 1K83L 3S1QL 5IYCL 5FLML 5C3EL 3M3YL 2E2JL 2WAQP 2JA5L 2R93L 5IP9L 5M5WL 4C3JL 4BY1L 3GTOL 3S14L 5IYBL 2NVTL 4A93L 4A3GL 3GTLL 1Y1VL 3S1NL 3HOUL 4A3DL 3GTQL 1I50L 4Y52L 3HOXL 2WB1P 1SFOL 3HOZL 1TWFL 4C3IL 4BY7L 4Y7NL 3RZDL 4A3IL 3S2DL 2JA8L 4BBRL 2JA7L 2E2IL 1R9TL 4C3HL 4BBSL 5M3FL 3HOVL 3HOYL 4A3LL 2JA6L 2YU9L 3S16L 5C4JL 2PMZP 5IP7L 3HKZP 4QIWP 3S2HL 2R92L 1WCML 3CQZL 3GTGL 4A3ML 4A3CL 3PO3L 1Y1WL 3H0GL 5FJ8L 4BXXL 1I3QL 4C2M1 5M5XL 3S15L 2NVQL 3HOWL 1TWCL 3GTKL 3I4NL 1TWAL 2NVYL 5C44L 5IYDL 4AYBP 3GTPL 3GTML 4A3JL 5M5YL 2VUML 3RZOL 3M4OL 2E2HL 4X6AL 4A3BL 3S17L 3GTJL 4A3EL 3PO2L 4A3KL 3S1ML
chains in the Genus database with same CATH superfamily
3S1RL 3H3VM 2EY4E 1R0IA 3K7AL 4AI3A 4JAEA 1TWHL 2R7ZL 1PFYA 2NVXL 1I6HL 3S1QL 4YWMA 4B8CD 3QQCE 3HJYB 3QVDA 2RFKB 4C3JL 4G6BA 3S14L 1YK4A 4A3GL 1P7PA 5AI3A 1Y1VL 3S1NL 1IU5A 1RWDA 1I50L 1RB9A 2WB1P 2V3BB 2MS3A 3HOZL 5MLC3 5H1Sc 4TVMA 2NYDA 1R9TL 5GADc 1B13A 4C3HL 3HOVL 1QCVA 2DSXA 5MF6A 1RYQA 3S16L 5C4JL 2CKAA 3HJWB 5IP7L 1YV1A 1R0HA 2PVEA 5GAEc 3CQZL 2JI3A 2V0FA 1IW7D 5JVH1 1LKMA 4BXXL 1ODHA 1QQTA 2K2DA 4E6YA 4POFA 1TWCL 1IRNA 1OWCA 1VZHA 1YUZA 4AYBP 1CAAA 2XJPA 2PVXA 5JVG1 8RXNA 3H99A 1JYBA 3M4OL 5MGNA 2KKDA 3S17L 4A3EL 4WFN1 4POGA 3S1ML 4TPUA 5C4XL 2GMGA 2A69D 1TWGL 1PZXA 2Z3RB 4ME3A 1T9QA 3I4ML 4A3FL 5DM71 4XXBB 1FHHA 4AI0A 5IYCL 5C3EL 5K2ME 2JA5L 5IY0A 3JR7A 2R93L 5M5WL 1S30A 4BY1L 1RDVA 2BE5D 5GAGc 3ZG6A 5MFPA 1BE7A 1CADA 3IU3I 3HOXL 2JI1A 2A6HD 1BRFA 1PFUA 3B08B 4UY81 1DX8A 3RZDL 2XJUA 2XJQA 3J7Z1 2JA7L 1DVBA 1SMUA 1VCXA 1B71A 4BBSL 5M3FL 3HOYL 2O5JD 2Z3QB 2ERSA 1BQ8A 2J9UB 2PMZP 1T9PA 4ZN1B 4QIWP 3S2HL 4AR4A 1BFYA 5FJ8L 4JAGA 5M5XL 2CR8A 3S15L 2NVQL 1LTLA 3A44A 2XJVA 2V0EA 5IYDL 3GTPL 1FHMA 1OWBA 2A68D 3GTML 4A3JL 2VL6A 3B0AB 1RYTA 3LWPB 2VUML 3RZOL 4AR5A 3LWQB 1WJVA 1NNQA 1S24A 4AI1A 1B2JA 3KYUA 5DM61 3P8BA 2C6AA 3LWRB 5AI2A 1YUXA 3LWOB 2A6ED 4JAFA 1F4LA 4JADA 5M3ML 3WWLA 4LHLA 1LKPA 6RXNA 1VZIA 2E2JL 2WAQP 1R0GA 1PFWA 1PFVA 2AYJA 4AHYA 3MSUA 3H9BA 5IYBL 1VZGA 2ERJA 3J7Y1 3LPEB 3GTLL 3PKJA 3HOUL 1LKOA 4A3DL 3KYWA 3GTQL 2KN9A 4Y52L 4C3IL 3WWNB 5MFZA 4A3IL 5EINC 2JA8L 4BBRL 2PSMC 3H97A 4A3LL 2YU9L 1T9OA 3HKZP 1WCML 1S2ZA 4A3CL 4RXNA 3H0GL 2JI2A 1I3QL 4C2M1 1B2OA 2QL0A 1H7VA 3KYXA 3I4NL 1TWAL 2NVYL 7RXNA 3P2AA 3HAXC 1R0FA 5M5YL 2M4YA 3PZAA 2PPTA 4XGHA 1Z92B 1NXEA 2ZIXA 2E2HL 3K35A 3PIP1 4A3BL 2C6BA 3PO2L 4A3KL 1IU6A 5EIOC 4AR6A 3VPBE 2B63L 3FKIL 2RDVA 4AHZA 1BQ9A 2Y0SP 3PKIA 2M6OA 1K83L 1R0JA 3SS2A 4K9FA 1C09A 5FLML 4GS7D 3FDJA 2HVYC 3M3YL 2M4VA 2HR5A 5IP9L 3GTOL 1RDGA 4AHWA 1YK5A 2NVTL 3PL5A 4A93L 1SMWA 2LCQA 2B5ID 1IROA 1SMMA 3PWFA 1SFOL 1E8JA 1TWFL 3LNLA 4BY7L 4Y7NL 3H9CA 1ZRPA 4V196 3PIO1 3S2DL 1NXGA 2E2IL 4AHXA 2PYAA 5GAHc 2JA6L 4AR3A 2R92L 3MPSA 3GTGL 2APOB 4A3ML 2XJSA 3KYYA 3PO3L 1Y1WL 2XJTA 3RZTA 2M6PA 2AUSB 3HOWL 3GTKL 4U671 2H12A 3LWVB 5C44L 2CKCA 2L0ZA 3RYGA 3NFPI 4YWLA 3RZ6A 5RXNA 2XJRA 4ZN3B 4AI2A 1QYBA 3KYVA 4LHNA 4X6AL 3MQKB 3GTJL 5AN9H 2AQCA
chains in the Genus database with same CATH topology
3S1RL 2B63L 3H3VM 5C4XL 1TWGL 3K7AL 3FKIL 1TWHL 2R7ZL 2Y0SP 2NVXL 5M3ML 3I4ML 4A3FL 1I6HL 1K83L 3S1QL 5IYCL 5FLML 5C3EL 3M3YL 2E2JL 2WAQP 2JA5L 2R93L 5IP9L 5M5WL 4C3JL 4BY1L 3GTOL 3S14L 5IYBL 2NVTL 4A93L 4A3GL 3GTLL 1Y1VL 3S1NL 3HOUL 4A3DL 3GTQL 1I50L 4Y52L 3HOXL 2WB1P 1SFOL 3HOZL 1TWFL 4C3IL 4BY7L 4Y7NL 3RZDL 4A3IL 3S2DL 2JA8L 4BBRL 2JA7L 2E2IL 1R9TL 4C3HL 4BBSL 5M3FL 3HOVL 3HOYL 4A3LL 2JA6L 2YU9L 3S16L 5C4JL 2PMZP 5IP7L 3HKZP 4QIWP 3S2HL 2R92L 1WCML 3CQZL 3GTGL 4A3ML 4A3CL 3PO3L 1Y1WL 3H0GL 5FJ8L 4BXXL 1I3QL 4C2M1 5M5XL 3S15L 2NVQL 3HOWL 1TWCL 3GTKL 3I4NL 1TWAL 2NVYL 5C44L 5IYDL 4AYBP 3GTPL 3GTML 4A3JL 5M5YL 2VUML 3RZOL 3M4OL 2E2HL 4X6AL 4A3BL 3S17L 3GTJL 4A3EL 3PO2L 4A3KL 3S1ML
chains in the Genus database with same CATH homology


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