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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molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
pubmed doi rcsb
source organism Saccharomyces cerevisiae (strain atcc 204508 / s288c)
molecule tags Transferase/dna/rna
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
4A3DL 5IP9L 1Y1VL 3HOYL 4A3KL 3S1QL 2R7ZL 2WB1P 3GTKL 3GTPL 1TWGL 5M5WL 3S2HL 4BY7L 4A3CL 5C44L 3RZDL 3HOWL 4A3IL 2Y0SP 3S2DL 4BBSL 3S14L 4X6AL 5IYDL 3S16L 1WCML 3HOUL 4C2M1 3GTLL 2NVQL 3H0GL 4A3BL 5C4XL 5M5YL 3M3YL 3S17L 5C3EL 4AYBP 3HKZP 3I4ML 5IYBL 1Y1WL 2WAQP 4C3IL 3PO2L 3GTJL 5IYCL 3S1NL 5IP7L 5C4JL 1TWCL 4A3JL 3CQZL 4C3HL 3GTGL 4Y52L 5M3FL 4A93L 3S1RL 2PMZP 1I6HL 1TWHL 4Y7NL 4BXXL 1R9TL 4QIWP 4BBRL 3HOVL 4BY1L 3S1ML 2E2IL 3FKIL 4A3GL 1SFOL 3GTOL 3M4OL 2JA5L 3PO3L 2JA7L 4A3ML 2YU9L 3S15L 2VUML 2NVYL 4A3FL 1TWFL 3GTML 4A3EL 4C3JL 2JA8L 2NVXL 1K83L 5FLML 2JA6L 2R92L 3RZOL 5M5XL 3GTQL 3K7AL 3H3VM 2E2HL 3HOZL 1I50L 3HOXL 5FJ8L 4A3LL 5M3ML 2B63L 2R93L 1TWAL 2E2JL 3I4NL 2NVTL 1I3QL
chains in the Genus database with same CATH superfamily
3RZ6A 5IP9L 1YUZA 3HOYL 2V0FA 4A3KL 3B08B 3J7Y1 5AI2A 3GTKL 2M6PA 3GTPL 1TWGL 5M5WL 3S2HL 4BY7L 4A3CL 4V196 2Y0SP 5MFPA 4BBSL 1LTLA 3A44A 1SMWA 2RDVA 3H9CA 4C2M1 3GTLL 2RFKB 4AI1A 5C3EL 5JVH1 3MSUA 5H1Sc 1BRFA 3PKIA 2V0EA 1T9OA 3LWQB 4XXBB 2PYAA 4K9FA 1CADA 1F4LA 3ZG6A 5IP7L 4AR3A 1T9QA 2Z3RB 4A3JL 5M3FL 4A93L 1TWHL 1FHMA 2XJRA 2V3BB 4BY1L 2E2IL 4JAEA 5MFZA 1DVBA 1YV1A 2JA5L 2PSMC 2C6BA 3RZTA 2YU9L 2NVYL 4A3FL 3MPSA 2KKDA 1VZGA 3JR7A 2K2DA 2JA8L 4JAGA 5MGNA 5M5XL 1RDGA 1RYQA 2LCQA 3K7AL 3HOXL 2CKAA 5M3ML 1QYBA 2XJSA 2R93L 1RYTA 3PIO1 3B0AB 3I4NL 1RDVA 4WFN1 1BQ9A 4A3DL 1SMUA 4GS7D 2HVYC 3FDJA 3NFPI 1PFUA 2XJVA 3LWOB 2A69D 3S1QL 1DX8A 1NNQA 3LWRB 5RXNA 5C44L 2JI1A 4LHLA 1R0JA 1P7PA 2VL6A 4TVMA 3S16L 1R0FA 1VZHA 1IW7D 1S30A 1BQ8A 3HOUL 3KYWA 4A3BL 5M5YL 3S17L 1NXGA 1NXEA 4AI3A 1PFYA 2XJTA 2WAQP 4C3IL 3PO2L 1RWDA 5IYCL 2PPTA 1TWCL 5MLC3 2O5JD 4C3HL 6RXNA 2C6AA 3S1RL 3QQCE 5MF6A 2H12A 2XJUA 3P2AA 3HJYB 3GTOL 1IROA 3PIP1 1VCXA 1IRNA 4AHYA 5GAHc 2VUML 1QQTA 1QCVA 3MQKB 5DM71 5AN9H 2XJQA 1T9PA 4POFA 5GAEc 3WWLA 5FLML 1K83L 2B5ID 2JA6L 3SS2A 3H3VM 2BE5D 3LWPB 4A3LL 2B63L 1YK5A 2CKCA 4G6BA 2ERSA 2A6ED 1I3QL 2AUSB 1YK4A 1PFVA 4POGA 2ZIXA 5GADc 1VZIA 3H9BA 2R7ZL 1IU5A 2WB1P 2QL0A 4ZN3B 3HOWL 4A3IL 3HJWB 3K35A 3S14L 4X6AL 2DSXA 2CR8A 1S2ZA 5IYDL 1R0GA 5K2ME 3HAXC 5IY0A 1PZXA 5C4XL 3M3YL 4JAFA 1B2JA 1C09A 1PFWA 5DM61 3H99A 1Y1WL 2J9UB 1R0IA 3GTJL 3S1NL 1RB9A 4UY81 4XGHA 3PWFA 3CQZL 4LHNA 1FHHA 2PMZP 4BXXL 1R9TL 2A6HD 4BBRL 3PL5A 3VPBE 3S1ML 4AR4A 3FKIL 4AI2A 4A3GL 3KYVA 1SFOL 3RYGA 2XJPA 1WJVA 7RXNA 3PO3L 2JI3A 4A3ML 2M4VA 1B71A 1LKOA 3KYYA 1TWFL 3GTML 2R92L 3RZOL 3PZAA 3GTQL 2M6OA 2E2HL 3HOZL 5EIOC 1I50L 5FJ8L 4YWMA 2L0ZA 1SMMA 3LNLA 4YWLA 4AHXA 1TWAL 5GAGc 2E2JL 2NVTL 1IU6A 2NYDA 1Y1VL 1OWCA 4JADA 8RXNA 2ERJA 2MS3A 4ME3A 3LPEB 4RXNA 2Z3QB 1H7VA 3RZDL 3S2DL 2PVEA 1S24A 3LWVB 1WCML 5JVG1 4AHZA 4TPUA 2NVQL 3H0GL 2KN9A 3PKJA 2EY4E 4AYBP 4ZN1B 3HKZP 1ODHA 1YUXA 2PVXA 1CAAA 3I4ML 5IYBL 1LKPA 5EINC 4AI0A 2HR5A 2A68D 4AR5A 5C4JL 3H97A 3GTGL 4Y52L 1I6HL 4Y7NL 4QIWP 3KYXA 4AHWA 3IU3I 1B13A 3HOVL 1E8JA 2JI2A 2AYJA 3M4OL 1BFYA 4AR6A 5AI3A 3KYUA 1R0HA 2JA7L 3S15L 2AQCA 1LKMA 1Z92B 2APOB 1JYBA 4A3EL 1OWBA 4C3JL 2NVXL 4B8CD 3WWNB 4U671 4E6YA 1ZRPA 3P8BA 1BE7A 3J7Z1 2GMGA 1B2OA 3QVDA 2M4YA
chains in the Genus database with same CATH topology
4A3DL 5IP9L 1Y1VL 3HOYL 4A3KL 3S1QL 2R7ZL 2WB1P 3GTKL 3GTPL 1TWGL 5M5WL 3S2HL 4BY7L 4A3CL 5C44L 3RZDL 3HOWL 4A3IL 2Y0SP 3S2DL 4BBSL 3S14L 4X6AL 5IYDL 3S16L 1WCML 3HOUL 4C2M1 3GTLL 2NVQL 3H0GL 4A3BL 5C4XL 5M5YL 3M3YL 3S17L 5C3EL 4AYBP 3HKZP 3I4ML 5IYBL 1Y1WL 2WAQP 4C3IL 3PO2L 3GTJL 5IYCL 3S1NL 5IP7L 5C4JL 1TWCL 4A3JL 3CQZL 4C3HL 3GTGL 4Y52L 5M3FL 4A93L 3S1RL 2PMZP 1I6HL 1TWHL 4Y7NL 4BXXL 1R9TL 4QIWP 4BBRL 3HOVL 4BY1L 3S1ML 2E2IL 3FKIL 4A3GL 1SFOL 3GTOL 3M4OL 2JA5L 3PO3L 2JA7L 4A3ML 2YU9L 3S15L 2VUML 2NVYL 4A3FL 1TWFL 3GTML 4A3EL 4C3JL 2JA8L 2NVXL 1K83L 5FLML 2JA6L 2R92L 3RZOL 5M5XL 3GTQL 3K7AL 3H3VM 2E2HL 3HOZL 1I50L 3HOXL 5FJ8L 4A3LL 5M3ML 2B63L 2R93L 1TWAL 2E2JL 3I4NL 2NVTL 1I3QL
chains in the Genus database with same CATH homology


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