3GTPL

Backtracked rna polymerase ii complex with 24mer 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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publication title Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
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 3gtpL00
5M5XL 3HKZP 5FJ8L 3GTQL 2B63L 4A93L 5M3FL 2NVQL 3S2DL 2PMZP 3H0GL 2E2JL 1TWHL 4A3IL 4X6AL 5IYCL 4A3JL 3S14L 5M5YL 3H3VM 4BBRL 4Y52L 4BBSL 2NVTL 2JA5L 2JA6L 3S1RL 3S1QL 2R93L 3GTOL 1R9TL 5IYDL 4A3EL 5IP9L 4C3HL 1I3QL 3HOZL 2E2IL 5IP7L 2E2HL 4A3LL 1I50L 5C3EL 2NVYL 3S2HL 1Y1VL 4A3DL 4Y7NL 3GTPL 4A3BL 4BY7L 4BXXL 2NVXL 1TWGL 5M5WL 1WCML 4C2M1 2JA8L 3GTKL 1TWCL 5C4XL 2R92L 5M3ML 1Y1WL 3GTJL 4A3KL 2YU9L 2WAQP 5C4JL 2VUML 3GTLL 1TWFL 3S15L 4C3IL 4A3ML 3GTML 2WB1P 4QIWP 2JA7L 3HOYL 3I4ML 3I4NL 3PO3L 1SFOL 3GTGL 3RZDL 3PO2L 5C44L 4BY1L 4AYBP 4A3GL 4C3JL 2Y0SP 1I6HL 3S16L 1K83L 3S1ML 3S17L 3CQZL 3K7AL 5FLML 3M4OL 3FKIL 5IYBL 3RZOL 3S1NL 3HOVL 3HOXL 3HOUL 4A3CL 4A3FL 3HOWL 2R7ZL 3M3YL 1TWAL
chains in the Genus database with same CATH superfamily
1T9PA 2C6AA 3FDJA 4YWLA 2B63L 2ZIXA 5M3FL 3J7Z1 1B2OA 2XJUA 4E6YA 2EY4E 2NVQL 1LTLA 2E2JL 1TWHL 4A3IL 4YWMA 1VCXA 3LWPB 2JI3A 3GTOL 3SS2A 1LKPA 3WWNB 2ERJA 3KYXA 3H97A 1I3QL 2NYDA 1I50L 3VPBE 5JVG1 5GAHc 1S24A 2NVYL 3NFPI 1H7VA 2NVXL 1VZIA 2JA8L 3GTKL 2AQCA 3MQKB 3LWOB 1B2JA 5C4XL 2R92L 4XXBB 5M3ML 3PKIA 1Y1WL 3GTJL 5MGNA 3H9BA 3S15L 2CKAA 3KYYA 4A3ML 4QIWP 3HOYL 3I4ML 3I4NL 3GTGL 2M6OA 5C44L 4BY1L 1DX8A 3RYGA 4A3GL 1B13A 4AHWA 1RWDA 3S17L 3CQZL 5GAEc 3FKIL 2XJSA 1DVBA 3RZOL 1BQ8A 1IW7D 1YV1A 2KN9A 3HOWL 4AHXA 1E8JA 3J7Y1 1VZHA 4AR6A 1BE7A 1OWBA 4A93L 2M4VA 3S2DL 2KKDA 2PMZP 3K35A 5K2ME 3H0GL 4X6AL 2Z3RB 3S14L 3H3VM 2M6PA 4AI1A 2JA6L 3S1RL 3S1QL 5IYDL 1RDGA 8RXNA 3KYVA 3H9CA 3H99A 1SMWA 3LWVB 1OWCA 4POGA 2E2IL 4WFN1 6RXNA 5C3EL 5DM71 3P2AA 3QQCE 1NNQA 1FHHA 1Y1VL 5EINC 1YK4A 1NXGA 7RXNA 3GTPL 2H12A 1C09A 4BXXL 2XJRA 1PFVA 1TWGL 3KYWA 1T9OA 5H1Sc 2RFKB 4A3KL 2WAQP 3GTLL 2VUML 4C3IL 2A6ED 5MFPA 1PFYA 2ERSA 2WB1P 4B8CD 5MLC3 2JA7L 3GTML 4ZN1B 1LKOA 4AR5A 5RXNA 3B08B 1QQTA 1IROA 4ME3A 4LHLA 1I6HL 3S16L 2C6BA 1K83L 3RZ6A 5FLML 3M4OL 1BQ9A 1SMUA 2A69D 2DSXA 3S1NL 3HOVL 3HOUL 3QVDA 4POFA 2R7ZL 3KYUA 2V0EA 1TWAL 1SMMA 2PPTA 1PFUA 1PFWA 5FJ8L 3GTQL 3PIP1 1YUXA 1S2ZA 4RXNA 1S30A 2RDVA 2O5JD 1VZGA 1RB9A 5M5YL 3A44A 2CR8A 1Z92B 1RDVA 1IU5A 4Y52L 5MF6A 2PSMC 5AN9H 2JA5L 4K9FA 1WJVA 2R93L 1T9QA 3MSUA 4AR3A 4A3EL 5IP9L 3LWRB 2J9UB 3HAXC 4AI2A 4ZN3B 4C3HL 3LWQB 5JVH1 2PYAA 5IP7L 2HR5A 4A3LL 4TPUA 1PZXA 3S2HL 4V196 3PL5A 4AR4A 3P8BA 1F4LA 1R0JA 1IRNA 2B5ID 1JYBA 5M5WL 1WCML 1TWCL 4JAFA 5AI3A 2V0FA 1YUZA 1R0GA 2XJTA 5C4JL 1TWFL 2AUSB 3LPEB 2K2DA 2XJVA 1QCVA 3RZDL 1BFYA 3PO2L 4LHNA 3RZTA 4AYBP 2Y0SP 2JI2A 3S1ML 3HJWB 4JAGA 2JI1A 4AHZA 1RYTA 2VL6A 4AI0A 4JAEA 5IYBL 2A6HD 1IU6A 3MPSA 1P7PA 5GAGc 3HOXL 4A3CL 5EIOC 4U671 1B71A 4A3FL 5MFZA 5M5XL 3HKZP 1CAAA 4UY81 1BRFA 2A68D 2HVYC 1R0IA 3WWLA 1ZRPA 2LCQA 3PZAA 3PIO1 2QL0A 1NXEA 3B0AB 5IYCL 4A3JL 4TVMA 4BBRL 3HJYB 2CKCA 4BBSL 5IY0A 2NVTL 1YK5A 1R9TL 2APOB 3JR7A 3PWFA 4AI3A 4GS7D 2GMGA 3HOZL 2E2HL 1LKMA 4A3DL 1CADA 4Y7NL 4A3BL 4BY7L 4G6BA 1FHMA 3LNLA 2MS3A 4C2M1 1R0FA 4JADA 2XJPA 2M4YA 5GADc 2BE5D 3IU3I 2V3BB 2YU9L 2Z3QB 1ODHA 2XJQA 4XGHA 3PO3L 1SFOL 2L0ZA 3ZG6A 3PKJA 5DM61 2AYJA 1QYBA 4C3JL 4AHYA 3K7AL 5AI2A 2PVXA 1RYQA 2PVEA 1R0HA 3M3YL
chains in the Genus database with same CATH topology
5M5XL 3HKZP 5FJ8L 3GTQL 2B63L 4A93L 5M3FL 2NVQL 3S2DL 2PMZP 3H0GL 2E2JL 1TWHL 4A3IL 4X6AL 5IYCL 4A3JL 3S14L 5M5YL 3H3VM 4BBRL 4Y52L 4BBSL 2NVTL 2JA5L 2JA6L 3S1RL 3S1QL 2R93L 3GTOL 1R9TL 5IYDL 4A3EL 5IP9L 4C3HL 1I3QL 3HOZL 2E2IL 5IP7L 2E2HL 4A3LL 1I50L 5C3EL 2NVYL 3S2HL 1Y1VL 4A3DL 4Y7NL 3GTPL 4A3BL 4BY7L 4BXXL 2NVXL 1TWGL 5M5WL 1WCML 4C2M1 2JA8L 3GTKL 1TWCL 5C4XL 2R92L 5M3ML 1Y1WL 3GTJL 4A3KL 2YU9L 2WAQP 5C4JL 2VUML 3GTLL 1TWFL 3S15L 4C3IL 4A3ML 3GTML 2WB1P 4QIWP 2JA7L 3HOYL 3I4ML 3I4NL 3PO3L 1SFOL 3GTGL 3RZDL 3PO2L 5C44L 4BY1L 4AYBP 4A3GL 4C3JL 2Y0SP 1I6HL 3S16L 1K83L 3S1ML 3S17L 3CQZL 3K7AL 5FLML 3M4OL 3FKIL 5IYBL 3RZOL 3S1NL 3HOVL 3HOXL 3HOUL 4A3CL 4A3FL 3HOWL 2R7ZL 3M3YL 1TWAL
chains in the Genus database with same CATH homology


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