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


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