5C4JL

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
Total Genus 3
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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
3
sequence length
43
structure length
43
Chain Sequence
b'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
molecule tags Transferase/dna/rna
total genus 3
structure length 43
sequence length 43
ec nomenclature
pdb deposition date 2015-06-18

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 5c4jL00
3GTOL 3M4OL 4AYBP 4C3IL 3S2HL 3S15L 3CQZL 1Y1WL 4C3JL 5C4JL 2JA8L 3HOVL 5M3FL 2E2HL 3S17L 2PMZP 3H0GL 3HOUL 2NVQL 4A3BL 3S1QL 2YU9L 4A3KL 3GTLL 5M5YL 3HOYL 3S16L 3FKIL 1I3QL 2E2IL 1Y1VL 2E2JL 3GTGL 1TWGL 2NVYL 3PO2L 3HOXL 2B63L 2Y0SP 5IP9L 5IYDL 4A3ML 4A3DL 3HKZP 4BY1L 3S2DL 2R93L 2R92L 4BXXL 4A3JL 4A3LL 4A93L 3GTML 4Y7NL 4BBRL 3GTJL 3I4ML 3HOWL 2WB1P 3S1NL 3RZOL 4A3FL 4BY7L 1WCML 3HOZL 4A3EL 5IYCL 2JA7L 5C4XL 4C3HL 3S14L 5FJ8L 1I50L 1TWFL 3RZDL 3GTKL 2NVTL 2JA6L 5M5WL 3H3VM 1TWHL 5IYBL 4BBSL 4A3IL 1TWCL 3S1ML 1SFOL 1TWAL 2VUML 4X6AL 4C2M1 3M3YL 2NVXL 1K83L 5M3ML 3S1RL 1R9TL 5C44L 3GTQL 4A3GL 2JA5L 5IP7L 5FLML 5M5XL 3GTPL 2WAQP 3PO3L 2R7ZL 3K7AL 1I6HL 3I4NL 4A3CL 5C3EL 4QIWP 4Y52L
chains in the Genus database with same CATH superfamily
5JVG1 5DM61 4AYBP 2PVEA 1SMMA 1T9OA 1LTLA 2M6PA 3HOVL 2E2HL 4LHNA 1NNQA 2A68D 3ZG6A 1Z92B 2V0FA 4A3BL 3B08B 2QL0A 1VZIA 1QQTA 2APOB 1ODHA 1ZRPA 2A6ED 3K35A 8RXNA 1TWGL 4AR6A 2PYAA 5IYDL 2PVXA 3S2DL 2VL6A 1LKMA 1RDGA 3LNLA 3LWQB 1BFYA 2V0EA 2MS3A 4A3FL 1DVBA 1LKOA 4RXNA 4A3EL 4XXBB 1PFYA 2C6BA 4AR3A 2RDVA 1I50L 2ZIXA 3PKJA 2XJQA 2JA6L 1CAAA 1YK5A 3RYGA 1F4LA 4AR5A 1B13A 2VUML 2NVXL 1K83L 5AI3A 2M4YA 3KYUA 2M6OA 1B71A 5IP7L 1FHHA 5EINC 3I4NL 5C3EL 1PZXA 5DM71 4C3IL 3S2HL 3S15L 1NXEA 3CQZL 3KYYA 4C3JL 5EIOC 5MGNA 2JA8L 1P7PA 4JADA 1C09A 3H97A 5JVH1 1S24A 3PWFA 5RXNA 1QCVA 3S17L 1PFWA 2XJUA 2PMZP 3HOUL 2ERSA 2H12A 3S1QL 3RZTA 2PPTA 2YU9L 2O5JD 2JI1A 5M5YL 4B8CD 3LWVB 2E2IL 4JAGA 1SMWA 2NVYL 3QVDA 3LWOB 2B63L 4YWMA 2KN9A 1OWCA 3P8BA 4YWLA 2LCQA 3HJWB 4BY1L 2CKAA 2K2DA 4G6BA 1VZHA 1R0IA 4A93L 4A3LL 2AYJA 4Y7NL 3KYVA 3GTJL 3HOWL 3S1NL 3QQCE 1R0FA 4BY7L 2JI2A 3HOZL 2XJVA 4AHZA 5GAHc 2GMGA 2PSMC 2JA7L 5C4XL 2A69D 1YV1A 1BE7A 4C3HL 3KYXA 2M4VA 4UY81 4JAFA 3IU3I 1TWFL 1RDVA 1T9QA 1OWBA 3H3VM 3PIO1 1TWHL 4A3IL 1TWCL 3J7Z1 4ME3A 3HAXC 4C2M1 3M3YL 1RYQA 3FDJA 5M3ML 5MFZA 4A3GL 5MLC3 5FLML 3PO3L 1B2OA 3K7AL 4AI0A 3WWNB 4AR4A 4A3CL 1PFUA 4QIWP 3GTOL 5K2ME 2AUSB 2HR5A 5C4JL 5M3FL 7RXNA 5GAEc 6RXNA 2V3BB 4LHLA 2NVQL 2BE5D 2JI3A 3JR7A 1S2ZA 2NYDA 4A3KL 3MPSA 3MQKB 3HOYL 2C6AA 1CADA 1Y1VL 3H99A 2E2JL 2XJPA 1IW7D 4AHWA 3PO2L 1IROA 2Y0SP 4A3ML 1T9PA 3PKIA 4A3DL 3HKZP 1WJVA 2R93L 1S30A 5MF6A 4A3JL 5AI2A 3GTML 3SS2A 3WWLA 3I4ML 3KYWA 3RZOL 4ZN3B 1SMUA 3A44A 1WCML 3VPBE 5IYCL 2HVYC 3LWPB 3PIP1 1BRFA 2DSXA 3S14L 1FHMA 1RWDA 3H9BA 2XJRA 1IRNA 5IYBL 4BBSL 4AI2A 5AN9H 1TWAL 1VZGA 3MSUA 4X6AL 2AQCA 4K9FA 1R9TL 5C44L 1BQ8A 1JYBA 1QYBA 3PZAA 1RB9A 3GTQL 1BQ9A 5M5XL 4TPUA 3GTPL 2R7ZL 1I6HL 2CR8A 3B0AB 4Y52L 4GS7D 3M4OL 2J9UB 5MFPA 2B5ID 2CKCA 4JAEA 4AI1A 2RFKB 1Y1WL 3J7Y1 1RYTA 2Z3QB 3LWRB 4U671 3NFPI 1YUXA 3H0GL 1YK4A 4POGA 3GTLL 3S16L 3FKIL 1I3QL 5GAGc 3RZ6A 3HJYB 2ERJA 3GTGL 3HOXL 5IP9L 4AHXA 4ZN1B 1R0HA 2R92L 2XJSA 3PL5A 4BXXL 2XJTA 5GADc 1IU6A 4AHYA 2KKDA 4E6YA 4BBRL 1PFVA 1IU5A 2WB1P 2A6HD 1R0GA 1H7VA 4XGHA 1E8JA 5FJ8L 1DX8A 3H9CA 3RZDL 2L0ZA 3GTKL 4TVMA 2NVTL 5M5WL 1R0JA 2Z3RB 3S1ML 1SFOL 1VCXA 4AI3A 1B2JA 3S1RL 1NXGA 1LKPA 5IY0A 2JA5L 3LPEB 2WAQP 4POFA 1YUZA 4WFN1 3P2AA 5H1Sc 4V196 2EY4E
chains in the Genus database with same CATH topology
3GTOL 3M4OL 4AYBP 4C3IL 3S2HL 3S15L 3CQZL 1Y1WL 4C3JL 5C4JL 2JA8L 3HOVL 5M3FL 2E2HL 3S17L 2PMZP 3H0GL 3HOUL 2NVQL 4A3BL 3S1QL 2YU9L 4A3KL 3GTLL 5M5YL 3HOYL 3S16L 3FKIL 1I3QL 2E2IL 1Y1VL 2E2JL 3GTGL 1TWGL 2NVYL 3PO2L 3HOXL 2B63L 2Y0SP 5IP9L 5IYDL 4A3ML 4A3DL 3HKZP 4BY1L 3S2DL 2R93L 2R92L 4BXXL 4A3JL 4A3LL 4A93L 3GTML 4Y7NL 4BBRL 3GTJL 3I4ML 3HOWL 2WB1P 3S1NL 3RZOL 4A3FL 4BY7L 1WCML 3HOZL 4A3EL 5IYCL 2JA7L 5C4XL 4C3HL 3S14L 5FJ8L 1I50L 1TWFL 3RZDL 3GTKL 2NVTL 2JA6L 5M5WL 3H3VM 1TWHL 5IYBL 4BBSL 4A3IL 1TWCL 3S1ML 1SFOL 1TWAL 2VUML 4X6AL 4C2M1 3M3YL 2NVXL 1K83L 5M3ML 3S1RL 1R9TL 5C44L 3GTQL 4A3GL 2JA5L 5IP7L 5FLML 5M5XL 3GTPL 2WAQP 3PO3L 2R7ZL 3K7AL 1I6HL 3I4NL 4A3CL 5C3EL 4QIWP 4Y52L
chains in the Genus database with same CATH homology


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