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


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