5C3EL

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
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
43
structure length
43
Chain Sequence
KYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR
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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 Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
pubmed doi rcsb
molecule tags Transferase/dna/rna
source organism Saccharomyces cerevisiae (strain atcc 204508 / s288c)
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 2
structure length 43
sequence length 43
ec nomenclature
pdb deposition date 2015-06-17

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 5c3eL00
4A3IL 3M3YL 4A3KL 1K83L 1TWGL 2R92L 2JA5L 5C3EL 3H3VM 5IYDL 3RZDL 3I4ML 3GTPL 3HOZL 1Y1VL 1I6HL 3GTKL 4A3ML 4BXXL 3S1QL 4A93L 1R9TL 5IP9L 4BY7L 5IYBL 4BBSL 4C3HL 4C3IL 3GTLL 3HOWL 3S15L 3S14L 4AYBP 2VUML 1TWCL 2JA8L 3S16L 1WCML 3S2HL 2R93L 2PMZP 1TWHL 3CQZL 5M5XL 3S1RL 2WB1P 5M3FL 2JA7L 1SFOL 3GTML 4BBRL 4C2M1 1I50L 4A3DL 4A3GL 1TWFL 4A3JL 3GTQL 3HKZP 3K7AL 3PO2L 5IP7L 5M3ML 2WAQP 3HOYL 4A3CL 5C4XL 3GTJL 1TWAL 2NVYL 2YU9L 4A3EL 3M4OL 3GTOL 4A3BL 2NVTL 3GTGL 5IYCL 5M5WL 2E2JL 3I4NL 5FJ8L 3PO3L 2NVQL 3H0GL 3S2DL 5M5YL 4Y7NL 2JA6L 3S1ML 2Y0SP 4QIWP 4A3FL 2B63L 2R7ZL 4BY1L 1I3QL 3HOVL 3RZOL 3HOXL 4X6AL 2NVXL 3FKIL 3HOUL 4A3LL 5C44L 4Y52L 3S17L 4C3JL 2E2HL 5FLML 5C4JL 1Y1WL 3S1NL 2E2IL
chains in the Genus database with same CATH superfamily
1IU6A 3KYXA 4UY81 4TVMA 1SMMA 1BQ8A 5GAGc 3H3VM 3LWQB 3RZDL 3GTPL 3PL5A 2ZIXA 1Y1VL 4JAEA 3HJWB 4AR5A 5IY0A 1R9TL 4AR4A 4BBSL 4C3IL 1B2OA 1S2ZA 2JA8L 1WCML 3CQZL 1OWCA 5M5XL 3S1RL 2HR5A 2XJPA 2JA7L 2V3BB 3MSUA 2Z3RB 2XJVA 4C2M1 2KN9A 4AR6A 1R0GA 2HVYC 5H1Sc 1C09A 4AHYA 2CR8A 3PWFA 4ME3A 4JAGA 1T9PA 1FHHA 5DM61 2DSXA 1S24A 3J7Y1 1CAAA 3H97A 1YUZA 1YK4A 1S30A 5MLC3 2E2JL 1RYQA 4YWLA 3H0GL 3S2DL 4A3FL 2B63L 2R7ZL 1B2JA 3RZOL 4POGA 2M4VA 2NVXL 3FKIL 4A3LL 5C44L 4Y52L 1RDVA 3S17L 3SS2A 2E2HL 5GAEc 3LNLA 2E2IL 1K83L 1TWGL 2R92L 1PZXA 2KKDA 5C3EL 5EINC 3GTKL 3S1QL 4AI2A 1CADA 1T9OA 2M6OA 2A6ED 5IP9L 3LWVB 3PKIA 5IYBL 3K35A 2O5JD 3GTLL 4AYBP 2VUML 2C6BA 1SMWA 3WWNB 1Z92B 1T9QA 1ZRPA 3KYWA 4XGHA 3LWOB 3H9CA 2XJSA 4POFA 3MQKB 2AQCA 1I50L 5MFZA 4A3DL 4A3GL 1DVBA 1R0HA 1YK5A 2ERJA 4K9FA 4A3JL 3KYUA 4JADA 3K7AL 2L0ZA 3HJYB 1RWDA 1JYBA 2A69D 1R0IA 1IRNA 3FDJA 2MS3A 2APOB 2VL6A 1IU5A 1IW7D 2Z3QB 1F4LA 2NVYL 2YU9L 3B0AB 3M4OL 3H99A 2AUSB 2NVTL 3WWLA 5GADc 2A68D 4XXBB 2CKCA 2GMGA 4ZN3B 1VZHA 4ZN1B 3PO3L 4LHLA 5AI3A 2JA6L 2LCQA 4QIWP 3JR7A 2BE5D 2QL0A 3NFPI 1QQTA 1FHMA 4AHWA 3S1NL 4AI1A 1PFYA 1IROA 3M3YL 5RXNA 4A3KL 3RZ6A 1H7VA 2J9UB 1E8JA 2V0EA 5MF6A 5IYDL 5MFPA 3I4ML 6RXNA 8RXNA 2JI1A 2XJUA 1I6HL 1SMUA 4A3ML 4A93L 2M4YA 1LKOA 2A6HD 1TWCL 1WJVA 1PFWA 1ODHA 1TWHL 1LTLA 3QQCE 2WB1P 3KYVA 1RYTA 5M3FL 1SFOL 1BFYA 1RDGA 3MPSA 3LWPB 3IU3I 1TWFL 1VCXA 4LHNA 3GTQL 1P7PA 2JI2A 3H9BA 2K2DA 2PYAA 2PPTA 5IP7L 5M3ML 4A3CL 3PKJA 1TWAL 1RB9A 5AN9H 4GS7D 3GTOL 3GTGL 3A44A 1QYBA 5IYCL 1YUXA 4YWMA 4TPUA 5DM71 4Y7NL 3S1ML 2Y0SP 4BY1L 4V196 1R0FA 3HOVL 1YV1A 4X6AL 3HOUL 3LPEB 1BQ9A 5FLML 5C4JL 2RDVA 4A3IL 3RYGA 1NXGA 4AI0A 1B71A 1QCVA 3LWRB 2JA5L 1DX8A 3P8BA 1R0JA 3HOZL 4B8CD 4BXXL 2CKAA 2V0FA 1VZIA 4BY7L 1PFVA 4C3HL 3HOWL 3S15L 7RXNA 3S14L 2ERSA 3P2AA 3ZG6A 1LKPA 3S16L 3S2HL 2R93L 2PMZP 1B13A 2XJTA 2B5ID 1BRFA 4E6YA 3GTML 2PSMC 4BBRL 2NYDA 5MGNA 5EIOC 4JAFA 3HKZP 5JVH1 3VPBE 3RZTA 3PO2L 1OWBA 1VZGA 5AI2A 3KYYA 3PZAA 2WAQP 3HOYL 5C4XL 4G6BA 3GTJL 2EY4E 2RFKB 4U671 2H12A 5K2ME 4RXNA 4A3EL 4A3BL 3B08B 2M6PA 4AHXA 3J7Z1 2JI3A 5M5WL 2C6AA 4AHZA 3QVDA 3I4NL 4AR3A 3PIO1 1BE7A 5FJ8L 2NVQL 5M5YL 4AI3A 1I3QL 2PVEA 1NXEA 3PIP1 2AYJA 2XJQA 1LKMA 3HOXL 3HAXC 2XJRA 5JVG1 4C3JL 1PFUA 5GAHc 2PVXA 1Y1WL 4WFN1 1NNQA
chains in the Genus database with same CATH topology
4A3IL 3M3YL 4A3KL 1K83L 1TWGL 2R92L 2JA5L 5C3EL 3H3VM 5IYDL 3RZDL 3I4ML 3GTPL 3HOZL 1Y1VL 1I6HL 3GTKL 4A3ML 4BXXL 3S1QL 4A93L 1R9TL 5IP9L 4BY7L 5IYBL 4BBSL 4C3HL 4C3IL 3GTLL 3HOWL 3S15L 3S14L 4AYBP 2VUML 1TWCL 2JA8L 3S16L 1WCML 3S2HL 2R93L 2PMZP 1TWHL 3CQZL 5M5XL 3S1RL 2WB1P 5M3FL 2JA7L 1SFOL 3GTML 4BBRL 4C2M1 1I50L 4A3DL 4A3GL 1TWFL 4A3JL 3GTQL 3HKZP 3K7AL 3PO2L 5IP7L 5M3ML 2WAQP 3HOYL 4A3CL 5C4XL 3GTJL 1TWAL 2NVYL 2YU9L 4A3EL 3M4OL 3GTOL 4A3BL 2NVTL 3GTGL 5IYCL 5M5WL 2E2JL 3I4NL 5FJ8L 3PO3L 2NVQL 3H0GL 3S2DL 5M5YL 4Y7NL 2JA6L 3S1ML 2Y0SP 4QIWP 4A3FL 2B63L 2R7ZL 4BY1L 1I3QL 3HOVL 3RZOL 3HOXL 4X6AL 2NVXL 3FKIL 3HOUL 4A3LL 5C44L 4Y52L 3S17L 4C3JL 2E2HL 5FLML 5C4JL 1Y1WL 3S1NL 2E2IL
chains in the Genus database with same CATH homology


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