5C4XL

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
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 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/rna/dna
total genus 3
structure length 44
sequence length 44
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 5c4xL00
2NVTL 1Y1VL 2R92L 4A3KL 4X6AL 3S2HL 3HOXL 3S1RL 5C44L 3H0GL 4C3JL 5C3EL 3FKIL 3GTPL 3K7AL 3GTOL 4A3BL 3GTGL 5M3ML 5IYDL 2WB1P 4BY1L 3HKZP 3S1ML 5FLML 5IYCL 4AYBP 4BBRL 3H3VM 2YU9L 3RZDL 3HOUL 3GTJL 1WCML 4A3GL 3GTQL 4A3CL 2PMZP 4BBSL 3S1QL 3GTKL 5C4XL 3HOVL 5IP7L 2JA7L 5IP9L 4A3DL 1TWCL 1K83L 3S2DL 4QIWP 4C3IL 3RZOL 3HOWL 4C2M1 2E2HL 2JA8L 3PO2L 4A93L 2JA6L 4Y7NL 3HOZL 2VUML 1SFOL 2Y0SP 2JA5L 1I3QL 1TWAL 5FJ8L 4A3ML 2WAQP 2NVYL 1Y1WL 2NVQL 4BY7L 4A3LL 3PO3L 4A3JL 3S1NL 5M5YL 3GTML 5M3FL 4C3HL 2E2JL 1R9TL 2NVXL 2E2IL 1TWHL 5IYBL 4A3EL 1I50L 2B63L 1TWGL 4Y52L 4A3FL 2R93L 1I6HL 3S14L 3GTLL 3M4OL 1TWFL 5M5WL 5M5XL 3HOYL 3I4NL 3M3YL 3I4ML 3S17L 3S16L 2R7ZL 3CQZL 4A3IL 4BXXL 5C4JL 3S15L
chains in the Genus database with same CATH superfamily
2NVTL 1CAAA 1QYBA 1LKMA 4AHWA 4A3KL 4AHZA 3S2HL 4ZN3B 3S1RL 3PZAA 4AHXA 3GTPL 2Z3QB 3GTOL 2PVXA 2Z3RB 3MSUA 4TPUA 1E8JA 2V0FA 2XJQA 1B13A 3KYXA 4ZN1B 4YWMA 2L0ZA 3GTJL 1WCML 4A3GL 2KKDA 2XJPA 4A3CL 5GAHc 1NNQA 3GTKL 3H99A 2BE5D 5C4XL 3HOVL 5IP7L 2JA7L 1CADA 2C6BA 5MFPA 4AR4A 3RYGA 2VUML 5MGNA 5DM71 2WAQP 1RWDA 2NVQL 5IY0A 3SS2A 1DX8A 1PFVA 4A3JL 2C6AA 1B2JA 2XJVA 3WWNB 2JI3A 5M3FL 2E2JL 6RXNA 3KYVA 5H1Sc 1R9TL 2E2IL 2A6ED 3LWRB 2B63L 1RB9A 4Y52L 2R93L 3M4OL 2M4YA 1NXEA 4G6BA 3HOYL 3I4ML 3S17L 5MF6A 3CQZL 4U671 3HJYB 1QCVA 1Y1VL 3JR7A 1PFYA 3HOXL 1B2OA 1LKOA 5C44L 3H0GL 1IROA 4C3JL 1YK4A 3FKIL 1FHMA 4BY1L 1IU6A 1IRNA 3LWOB 1T9QA 5IYCL 3H3VM 1YUXA 5JVG1 2M6OA 2APOB 2XJTA 2PVEA 1T9PA 5GADc 1LKPA 2HR5A 1PFWA 1BQ9A 1BFYA 4BBSL 3KYWA 4AR5A 1R0JA 4JADA 3LWQB 5MFZA 3LWVB 4AI0A 2K2DA 2E2HL 2JA8L 3PO2L 4A93L 2JA6L 1RDVA 2JA5L 1I3QL 3PKJA 1S2ZA 3B0AB 1ZRPA 1H7VA 2VL6A 5GAGc 3KYYA 1SMWA 3RZ6A 3QVDA 1S30A 4XGHA 3K35A 4E6YA 4AI2A 2QL0A 1OWBA 5IYBL 1TWGL 1I6HL 3GTLL 4JAFA 2NYDA 3H97A 4AI1A 5M5XL 1SMMA 5DM61 2V3BB 2A68D 3H9CA 5C4JL 3IU3I 3LWPB 3KYUA 3PKIA 1PZXA 1IU5A 1B71A 3VPBE 5AI3A 5C3EL 2M4VA 2JI1A 4A3BL 1VZGA 3NFPI 3GTGL 5M3ML 1VCXA 3HKZP 3S1ML 3LPEB 2O5JD 5AI2A 2M6PA 3PIO1 5JVH1 1ODHA 4LHLA 4AYBP 3QQCE 2XJUA 3RZDL 5AN9H 3WWLA 3PL5A 3HOUL 2PPTA 1C09A 3GTQL 4AI3A 3RZTA 3S1QL 3J7Z1 4A3DL 1K83L 3S2DL 5EINC 4JAGA 4C3IL 3HJWB 1VZHA 3HOZL 1RDGA 2Y0SP 1TWAL 8RXNA 2HVYC 1SMUA 2MS3A 4A3ML 3A44A 2NVYL 1Y1WL 2JI2A 4BY7L 4POGA 3PO3L 1BRFA 3S1NL 2RFKB 1YV1A 1RYTA 2A69D 2A6HD 3GTML 2AYJA 1R0GA 1RYQA 2CKCA 1OWCA 1QQTA 2EY4E 2XJSA 1IW7D 1I50L 4WFN1 2AUSB 1TWFL 4TVMA 5M5WL 3I4NL 3M3YL 5RXNA 4JAEA 5K2ME 2PYAA 4BXXL 2CR8A 2KN9A 1BE7A 3B08B 2R92L 1NXGA 1JYBA 4X6AL 1R0FA 4LHNA 2CKAA 2XJRA 4UY81 2ERSA 7RXNA 3K7AL 3PWFA 1LTLA 2WB1P 5IYDL 3J7Y1 1R0HA 5FLML 1F4LA 4GS7D 4BBRL 1WJVA 2YU9L 4AR3A 5EIOC 3LNLA 1PFUA 1S24A 2J9UB 2B5ID 2GMGA 2PMZP 1YK5A 1Z92B 2V0EA 3P8BA 5IP9L 3FDJA 1YUZA 1VZIA 4POFA 4RXNA 1R0IA 2H12A 1TWCL 4ME3A 4QIWP 3RZOL 3HOWL 4C2M1 4B8CD 2RDVA 5GAEc 4Y7NL 1FHHA 1SFOL 5FJ8L 3P2AA 3ZG6A 1BQ8A 2PSMC 2ERJA 2DSXA 4A3LL 3MPSA 5M5YL 1T9OA 4AHYA 3H9BA 4V196 5MLC3 4C3HL 3MQKB 4XXBB 1P7PA 2NVXL 3PIP1 1TWHL 4A3EL 4A3FL 2LCQA 3S14L 4YWLA 2ZIXA 4AR6A 3HAXC 2AQCA 2R7ZL 3S16L 1DVBA 4K9FA 4A3IL 3S15L
chains in the Genus database with same CATH topology
2NVTL 1Y1VL 2R92L 4A3KL 4X6AL 3S2HL 3HOXL 3S1RL 5C44L 3H0GL 4C3JL 5C3EL 3FKIL 3GTPL 3K7AL 3GTOL 4A3BL 3GTGL 5M3ML 5IYDL 2WB1P 4BY1L 3HKZP 3S1ML 5FLML 5IYCL 4AYBP 4BBRL 3H3VM 2YU9L 3RZDL 3HOUL 3GTJL 1WCML 4A3GL 3GTQL 4A3CL 2PMZP 4BBSL 3S1QL 3GTKL 5C4XL 3HOVL 5IP7L 2JA7L 5IP9L 4A3DL 1TWCL 1K83L 3S2DL 4QIWP 4C3IL 3RZOL 3HOWL 4C2M1 2E2HL 2JA8L 3PO2L 4A93L 2JA6L 4Y7NL 3HOZL 2VUML 1SFOL 2Y0SP 2JA5L 1I3QL 1TWAL 5FJ8L 4A3ML 2WAQP 2NVYL 1Y1WL 2NVQL 4BY7L 4A3LL 3PO3L 4A3JL 3S1NL 5M5YL 3GTML 5M3FL 4C3HL 2E2JL 1R9TL 2NVXL 2E2IL 1TWHL 5IYBL 4A3EL 1I50L 2B63L 1TWGL 4Y52L 4A3FL 2R93L 1I6HL 3S14L 3GTLL 3M4OL 1TWFL 5M5WL 5M5XL 3HOYL 3I4NL 3M3YL 3I4ML 3S17L 3S16L 2R7ZL 3CQZL 4A3IL 4BXXL 5C4JL 3S15L
chains in the Genus database with same CATH homology


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