5C4JL

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

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
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...