3GTKL

Backtracked rna polymerase ii complex with 18mer rna
Total Genus 2
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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
2
sequence length
46
structure length
46
Chain Sequence
ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR
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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 Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
pubmed doi rcsb
molecule tags Transcription, transferase/dna-rna hybrid
total genus 2
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2009-03-27

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 3gtkL00
2R93L 3S1ML 1I50L 2JA6L 1Y1VL 2VUML 4Y7NL 1TWFL 3HOUL 2JA5L 4BBRL 2NVYL 2E2IL 4A3CL 3HOWL 3GTLL 5FJ8L 5C44L 4A3IL 3FKIL 2JA8L 3S17L 2JA7L 5M5XL 2YU9L 3S1QL 3HOVL 4QIWP 2NVXL 4BY7L 3I4ML 4A3ML 2WAQP 3M3YL 3S2HL 3RZDL 1K83L 2R7ZL 3I4NL 2NVTL 3S16L 5M3ML 3HOYL 5FLML 2E2HL 2E2JL 3GTQL 4C3IL 3PO2L 5C3EL 5IP9L 3HKZP 1I3QL 2NVQL 5IYDL 4A93L 4A3JL 4A3EL 4BY1L 4C3JL 4A3LL 3CQZL 3GTML 4A3BL 2B63L 5M5YL 3S14L 1WCML 3K7AL 5IYCL 5IP7L 1TWAL 3RZOL 1I6HL 3S15L 4Y52L 4A3DL 5M3FL 2WB1P 1TWCL 3S1NL 3HOXL 1TWGL 3S2DL 3GTKL 5C4JL 4C2M1 4C3HL 4A3GL 3GTJL 4BXXL 3GTGL 2Y0SP 3H0GL 1SFOL 3GTPL 2PMZP 4AYBP 5C4XL 5M5WL 3HOZL 3S1RL 4X6AL 1R9TL 3H3VM 3GTOL 1TWHL 1Y1WL 4A3FL 2R92L 3PO3L 4BBSL 5IYBL 3M4OL 4A3KL
chains in the Genus database with same CATH superfamily
5EINC 2CKCA 4LHNA 1VZGA 3LWOB 1TWFL 3HOUL 1B13A 2JA5L 2DSXA 4JAEA 1VCXA 3HOWL 1H7VA 3LPEB 4AHXA 3S17L 2JA7L 2A68D 4E6YA 1SMWA 4ZN1B 4QIWP 3QQCE 2EY4E 3JR7A 3I4ML 1RDGA 3S2HL 1LKMA 3H97A 2XJRA 4AI2A 1R0IA 1RDVA 5M3ML 3HOYL 2E2HL 2AYJA 1P7PA 3FDJA 1YV1A 1YK4A 2HVYC 5IP9L 3HAXC 1T9PA 1I3QL 4A3EL 4A3LL 3PL5A 2HR5A 1NXEA 1Z92B 5MLC3 4YWMA 2C6BA 1CAAA 1IRNA 1TWAL 3KYWA 4Y52L 3B08B 4ME3A 4RXNA 3HOXL 3GTKL 2APOB 3LNLA 5C4JL 2BE5D 4A3GL 4WFN1 1YK5A 4POFA 2Y0SP 1SFOL 4V196 2PMZP 3J7Y1 2B5ID 5C4XL 3HOZL 3S1RL 1TWHL 1FHHA 1ZRPA 3M4OL 2ERJA 2XJUA 4A3KL 2JI2A 4AR5A 3S1ML 3LWPB 2PSMC 2VUML 2A6ED 2KKDA 1SMUA 1R0JA 3QVDA 1R0FA 2NVYL 3RZ6A 5K2ME 2E2IL 2LCQA 1B2JA 4JAFA 5DM71 4XGHA 3RZTA 3GTLL 5FJ8L 5C44L 1NXGA 5M5XL 1QQTA 2YU9L 2VL6A 3M3YL 2A69D 3PIP1 2R7ZL 3I4NL 1PFYA 3S16L 1RYQA 4AI3A 1BQ8A 3IU3I 2CKAA 3PO2L 1QCVA 1VZIA 4BY1L 3CQZL 5RXNA 2XJQA 2B63L 1IROA 1WCML 2M6PA 3LWRB 5IYCL 5GADc 1PFVA 1I6HL 1T9OA 5AN9H 3H9CA 4G6BA 1TWCL 2H12A 1TWGL 3S2DL 2XJPA 5H1Sc 2O5JD 4C2M1 3NFPI 4JADA 3KYYA 1FHMA 1YUXA 3MPSA 4AI1A 1QYBA 2Z3RB 5AI3A 4AYBP 5MF6A 3HJWB 4X6AL 5DM61 2JI1A 5MFZA 3GTOL 4A3FL 2RFKB 1PFWA 3J7Z1 2V0FA 3A44A 3MQKB 2A6HD 7RXNA 2QL0A 2R93L 2PYAA 1Y1VL 2XJSA 1S30A 3PIO1 4BBRL 4JAGA 1RYTA 4LHLA 4A3CL 1RWDA 1IU5A 2M4VA 2ERSA 4A3IL 3FKIL 1SMMA 1BFYA 3S1QL 4AR6A 5GAGc 2WAQP 6RXNA 4AI0A 3HJYB 3KYUA 2NVTL 1BQ9A 4YWLA 2AQCA 2E2JL 1LKPA 3GTQL 4C3IL 4TPUA 5C3EL 1F4LA 2Z3QB 5IYDL 4A93L 4A3JL 1T9QA 5GAEc 3H9BA 3GTML 4A3BL 1PZXA 3ZG6A 3P8BA 1E8JA 3K7AL 2KN9A 8RXNA 5IP7L 3RZOL 3S15L 2NYDA 4A3DL 5M3FL 2WB1P 3KYXA 3S1NL 3H99A 4UY81 1RB9A 2M6OA 1PFUA 3KYVA 1IU6A 4BXXL 4AHWA 4POGA 3RYGA 3H0GL 2GMGA 1R0HA 5M5WL 2PVXA 1R9TL 3H3VM 1LTLA 3PKIA 2PVEA 2R92L 3PO3L 4BBSL 1OWCA 5IYBL 4GS7D 3B0AB 1S24A 1I50L 2JA6L 4AHYA 2L0ZA 4Y7NL 5IY0A 1BRFA 4TVMA 4K9FA 1B71A 3VPBE 2V0EA 2K2DA 1S2ZA 1DVBA 4ZN3B 5GAHc 4XXBB 2XJTA 1ODHA 2JA8L 2M4YA 3P2AA 2RDVA 4AHZA 3HOVL 2PPTA 3WWLA 2NVXL 3PZAA 4BY7L 4A3ML 5JVG1 3LWQB 3RZDL 1K83L 1VZHA 3LWVB 5FLML 1B2OA 3WWNB 3HKZP 1DX8A 2CR8A 2NVQL 1OWBA 4C3JL 5AI2A 2JI3A 3K35A 4AR4A 2V3BB 1LKOA 1WJVA 5M5YL 4AR3A 4U671 3S14L 1CADA 1BE7A 5JVH1 5MFPA 5EIOC 1C09A 1JYBA 1IW7D 2AUSB 2XJVA 1YUZA 4C3HL 3GTJL 4B8CD 3MSUA 3GTGL 2ZIXA 1R0GA 3PKJA 3PWFA 5MGNA 3GTPL 1NNQA 3SS2A 2MS3A 1Y1WL 2J9UB 2C6AA
chains in the Genus database with same CATH topology
2R93L 3S1ML 1I50L 2JA6L 1Y1VL 2VUML 4Y7NL 1TWFL 3HOUL 2JA5L 4BBRL 2NVYL 2E2IL 4A3CL 3HOWL 3GTLL 5FJ8L 5C44L 4A3IL 3FKIL 2JA8L 3S17L 2JA7L 5M5XL 2YU9L 3S1QL 3HOVL 4QIWP 2NVXL 4BY7L 3I4ML 4A3ML 2WAQP 3M3YL 3S2HL 3RZDL 1K83L 2R7ZL 3I4NL 2NVTL 3S16L 5M3ML 3HOYL 5FLML 2E2HL 2E2JL 3GTQL 4C3IL 3PO2L 5C3EL 5IP9L 3HKZP 1I3QL 2NVQL 5IYDL 4A93L 4A3JL 4A3EL 4BY1L 4C3JL 4A3LL 3CQZL 3GTML 4A3BL 2B63L 5M5YL 3S14L 1WCML 3K7AL 5IYCL 5IP7L 1TWAL 3RZOL 1I6HL 3S15L 4Y52L 4A3DL 5M3FL 2WB1P 1TWCL 3S1NL 3HOXL 1TWGL 3S2DL 3GTKL 5C4JL 4C2M1 4C3HL 4A3GL 3GTJL 4BXXL 3GTGL 2Y0SP 3H0GL 1SFOL 3GTPL 2PMZP 4AYBP 5C4XL 5M5WL 3HOZL 3S1RL 4X6AL 1R9TL 3H3VM 3GTOL 1TWHL 1Y1WL 4A3FL 2R92L 3PO3L 4BBSL 5IYBL 3M4OL 4A3KL
chains in the Genus database with same CATH homology


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