5C4JL

Crystal structure of a transcribing rna polymerase ii complex reveals a complete transcription bubble
Total Genus 3

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

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
EMPTYS1 (30-31)TIV1 (31-34)Updating...
connected with : NaN
molecule tags Transferase/dna/rna
publication title Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
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
1TWHL 5C3EL 4A3GL 2WAQP 3H0GL 3S16L 1WCML 3HKZP 3FKIL 2JA7L 3K7AL 5IYBL 5C44L 5C4JL 3HOYL 3HOZL 3H3VM 3M4OL 2E2HL 2NVXL 2JA5L 4C2M1 1TWFL 2B63L 4A3EL 2NVYL 5IYDL 2PMZP 4A3ML 1R9TL 3CQZL 3S15L 2NVTL 3PO3L 4A3BL 3HOVL 3S1ML 2E2JL 5FLML 3S2DL 4A3JL 1K83L 2R92L 2VUML 3S1RL 4BY7L 4AYBP 3GTPL 3GTKL 4BXXL 1TWGL 3HOWL 2YU9L 5IYCL 4X6AL 2JA6L 4A3CL 3PO2L 1I6HL 3S17L 5M5YL 4Y7NL 4BY1L 4C3IL 1I3QL 4A3LL 4A3DL 3GTLL 3HOXL 4C3JL 5M3FL 3RZOL 4Y52L 5M5WL 1TWCL 5IP7L 3S1NL 3S2HL 1Y1VL 2R7ZL 5FJ8L 4A93L 4A3KL 3GTQL 3GTJL 4A3FL 4BBSL 2R93L 5C4XL 3M3YL 3GTOL 2Y0SP 3I4NL 3RZDL 3S1QL 4QIWP 4BBRL 2JA8L 4C3HL 1SFOL 3S14L 5M3ML 1TWAL 5M5XL 3GTGL 3HOUL 2WB1P 2NVQL 3I4ML 1I50L 2E2IL 5IP9L 4A3IL 1Y1WL 3GTML
chains in the Genus database with same CATH superfamily
2QL0A 3H0GL 2NYDA 3FKIL 2JA7L 4XGHA 5AI2A 3HOYL 4ZN1B 3M4OL 4C2M1 3MSUA 3WWNB 5IYDL 2PMZP 1R9TL 2CKCA 3SS2A 3CQZL 5MFPA 1IU5A 3KYXA 5MF6A 3PO3L 1CADA 3KYVA 3S2DL 2M6PA 1R0IA 2R92L 4BY7L 3B0AB 3LWOB 4JAFA 1LKMA 2HR5A 2RFKB 5AI3A 2C6BA 1TWGL 5EIOC 1PZXA 3RZ6A 4X6AL 3H9BA 1WJVA 1PFUA 2H12A 3PIP1 1S30A 4A3DL 1S24A 5EINC 2XJVA 1JYBA 3P8BA 5M5WL 3PKJA 7RXNA 3S2HL 2GMGA 2AYJA 2VL6A 4A3FL 4RXNA 3M3YL 2Y0SP 4AI2A 5M5XL 1VZHA 1SMUA 2AUSB 5IP9L 4A3GL 3MQKB 2PPTA 3LWVB 1WCML 2BE5D 3K7AL 3LWQB 1R0FA 3QQCE 5MLC3 3MPSA 3PWFA 1T9PA 3H3VM 4AR6A 2PVXA 2NVXL 4YWMA 1E8JA 1NXGA 2B63L 1PFVA 2A6ED 4A3EL 2NVYL 3J7Y1 2Z3QB 5DM61 2NVTL 1YUZA 3H99A 1LTLA 1VZGA 1PFYA 3LNLA 4XXBB 1B2OA 1RDGA 4A3JL 1K83L 3S1RL 1CAAA 4AYBP 4AHXA 2M4YA 1FHHA 3GTPL 3GTKL 1T9QA 4B8CD 4TPUA 1YV1A 4V196 4A3CL 3HAXC 4K9FA 3S17L 2KN9A 4Y7NL 1OWCA 3FDJA 1OWBA 2XJSA 2ZIXA 2XJPA 2J9UB 3P2AA 4Y52L 4GS7D 1ODHA 1S2ZA 2V0FA 5GAGc 1BFYA 2R7ZL 4A3KL 2R93L 4BBSL 4AR4A 1NNQA 3RZDL 4QIWP 4AI0A 4C3HL 4YWLA 3S14L 2WB1P 3IU3I 2NVQL 1F4LA 1BQ9A 2PYAA 1Y1WL 3GTML 1TWHL 2JI2A 5C3EL 1YK5A 5GAHc 2WAQP 4ME3A 1BE7A 1ZRPA 5C4JL 3PL5A 4AR3A 2CR8A 2XJRA 2K2DA 2E2HL 2A69D 2M6OA 2JA5L 1TWFL 3H9CA 3H97A 2EY4E 1B71A 4A3ML 1VZIA 2V0EA 3S15L 2LCQA 4JAEA 1RYQA 4POFA 3HOVL 4U671 2VUML 1IRNA 4AI3A 4AHZA 1YK4A 2CKAA 3KYWA 8RXNA 1RYTA 3HOWL 2M4VA 4JADA 5IYCL 6RXNA 1NXEA 2JA6L 2Z3RB 1I6HL 3VPBE 5M5YL 3QVDA 4G6BA 4BY1L 4C3IL 1I3QL 1Z92B 1QQTA 3PKIA 4C3JL 4JAGA 5M3FL 2ERSA 3RZOL 5K2ME 1TWCL 5IP7L 1R0HA 3A44A 4A93L 4LHLA 5DM71 3GTJL 2XJTA 3I4NL 4BBRL 2XJUA 1P7PA 3JR7A 1SFOL 1BRFA 2HVYC 5AN9H 1C09A 3HOUL 3I4ML 1I50L 2C6AA 2JI3A 2RDVA 4A3IL 3S16L 3HJWB 2APOB 2ERJA 3HKZP 3KYYA 5GADc 5JVG1 1B13A 5IYBL 5C44L 4POGA 4LHNA 3LWPB 3HOZL 1LKPA 1R0JA 3ZG6A 3HJYB 2DSXA 3PZAA 1IW7D 4AHWA 1H7VA 3B08B 4TVMA 1RWDA 4AHYA 5RXNA 1LKOA 1T9OA 3RYGA 2XJQA 1R0GA 4A3BL 3S1ML 2E2JL 1DX8A 5FLML 1RDVA 3WWLA 5JVH1 2AQCA 2A6HD 4AR5A 4BXXL 4UY81 2YU9L 1VCXA 2V3BB 3LPEB 3PO2L 5MGNA 1QYBA 3KYUA 2O5JD 1SMWA 3K35A 4A3LL 4ZN3B 3GTLL 1FHMA 1QCVA 3HOXL 1IU6A 5MFZA 2MS3A 4WFN1 3J7Z1 3S1NL 1DVBA 1Y1VL 5FJ8L 5GAEc 3GTQL 2PSMC 1BQ8A 4E6YA 5C4XL 2KKDA 1SMMA 2PVEA 3GTOL 1YUXA 3S1QL 2JA8L 2B5ID 1IROA 3RZTA 5M3ML 1TWAL 2A68D 2L0ZA 5IY0A 1B2JA 3GTGL 1PFWA 3LWRB 2JI1A 2E2IL 1RB9A 3NFPI 4AI1A 3PIO1 5H1Sc
chains in the Genus database with same CATH topology
1TWHL 5C3EL 4A3GL 2WAQP 3H0GL 3S16L 1WCML 3HKZP 3FKIL 2JA7L 3K7AL 5IYBL 5C44L 5C4JL 3HOYL 3HOZL 3H3VM 3M4OL 2E2HL 2NVXL 2JA5L 4C2M1 1TWFL 2B63L 4A3EL 2NVYL 5IYDL 2PMZP 4A3ML 1R9TL 3CQZL 3S15L 2NVTL 3PO3L 4A3BL 3HOVL 3S1ML 2E2JL 5FLML 3S2DL 4A3JL 1K83L 2R92L 2VUML 3S1RL 4BY7L 4AYBP 3GTPL 3GTKL 4BXXL 1TWGL 3HOWL 2YU9L 5IYCL 4X6AL 2JA6L 4A3CL 3PO2L 1I6HL 3S17L 5M5YL 4Y7NL 4BY1L 4C3IL 1I3QL 4A3LL 4A3DL 3GTLL 3HOXL 4C3JL 5M3FL 3RZOL 4Y52L 5M5WL 1TWCL 5IP7L 3S1NL 3S2HL 1Y1VL 2R7ZL 5FJ8L 4A93L 4A3KL 3GTQL 3GTJL 4A3FL 4BBSL 2R93L 5C4XL 3M3YL 3GTOL 2Y0SP 3I4NL 3RZDL 3S1QL 4QIWP 4BBRL 2JA8L 4C3HL 1SFOL 3S14L 5M3ML 1TWAL 5M5XL 3GTGL 3HOUL 2WB1P 2NVQL 3I4ML 1I50L 2E2IL 5IP9L 4A3IL 1Y1WL 3GTML
chains in the Genus database with same CATH homology


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