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


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