3GTLL

Backtracked rna polymerase ii complex with 13mer with g<>u mismatch
Total Genus 1
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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
1
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 1
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 3gtlL00
4AYBP 3FKIL 1TWHL 3GTML 4QIWP 3S14L 4A93L 4A3LL 3HOWL 3HOXL 5C3EL 2E2JL 3S1ML 2Y0SP 4A3GL 3PO3L 4Y7NL 4A3KL 3M4OL 3S1NL 1WCML 2NVXL 5IP7L 1TWGL 3PO2L 5IYCL 4A3BL 3H3VM 1I6HL 2JA8L 3I4NL 4C3HL 1TWAL 5C44L 4A3JL 3GTOL 3GTQL 2B63L 4A3ML 5M3ML 1TWCL 3S16L 1I50L 3K7AL 2WAQP 3GTPL 5FJ8L 3HOZL 4X6AL 3S17L 2PMZP 5IYBL 2NVYL 4BBRL 5C4XL 1Y1VL 3S1RL 1R9TL 3HOYL 2E2HL 3H0GL 4BXXL 4A3CL 3I4ML 3GTJL 4C3JL 2YU9L 2R7ZL 4A3EL 3HOUL 5IYDL 5M3FL 2VUML 3GTLL 4BY7L 4A3IL 1I3QL 5M5WL 2WB1P 3GTGL 5M5YL 3S2DL 4BBSL 2R93L 3S2HL 5C4JL 2R92L 3HKZP 4A3FL 5FLML 5M5XL 2JA7L 2JA6L 5IP9L 4BY1L 3RZOL 4C3IL 2JA5L 4Y52L 1K83L 3S1QL 3RZDL 3CQZL 3M3YL 3S15L 3GTKL 2NVQL 1TWFL 4C2M1 3HOVL 2E2IL 1SFOL 2NVTL 1Y1WL 4A3DL
chains in the Genus database with same CATH superfamily
2NYDA 3GTML 4XXBB 4A93L 1R0FA 5C3EL 4ME3A 3HAXC 4YWLA 3PKIA 5MLC3 1WCML 5K2ME 3P8BA 2JA8L 3I4NL 4C3HL 3P2AA 4JAGA 5M3ML 1TWCL 1I50L 1VZHA 4ZN3B 5FJ8L 5EINC 2EY4E 2KKDA 3LWVB 2E2HL 4E6YA 8RXNA 2XJVA 4JAFA 2JI1A 3GTJL 2M4YA 2YU9L 6RXNA 2CKAA 5DM71 3HOUL 2APOB 1E8JA 5M3FL 2PVXA 1YV1A 2XJPA 1NNQA 5M5WL 3LPEB 1LKMA 5JVG1 1F4LA 5C4JL 2Z3QB 5FLML 2JA5L 2HR5A 3JR7A 1YUZA 3RZDL 2V3BB 2AYJA 4AHWA 1JYBA 2RDVA 3H99A 2M6OA 1Y1WL 4A3DL 2JI3A 3B0AB 5EIOC 1TWHL 4TVMA 3WWLA 2PPTA 4AHYA 3HOXL 1S2ZA 1CAAA 4JAEA 2BE5D 1PZXA 1C09A 4POGA 4A3KL 2NVXL 5IP7L 1TWGL 5IYCL 5GADc 1VCXA 3A44A 1I6HL 4A3JL 1RWDA 2M6PA 3S16L 3K7AL 3RZ6A 5AN9H 1CADA 2XJTA 1RDGA 4X6AL 3S17L 3IU3I 5AI2A 5IYBL 4K9FA 4AR6A 1T9QA 1R0IA 3S1RL 2DSXA 1QYBA 3H9BA 4BXXL 2RFKB 1YK5A 3VPBE 4A3CL 1ZRPA 1T9PA 4V196 4GS7D 3PKJA 4LHLA 5IYDL 2VUML 3QVDA 1BRFA 3LWQB 5M5YL 4BBSL 4ZN1B 1DVBA 2R93L 2A6ED 2VL6A 1S24A 4JADA 3MPSA 1LTLA 2R92L 1R0GA 3H97A 1RYTA 2A69D 3ZG6A 5MFPA 2JA6L 5IP9L 4BY1L 3RZOL 2C6AA 4C3IL 4Y52L 2V0EA 3LNLA 3S1QL 1R0HA 3M3YL 3GTKL 2CKCA 2NVQL 1IRNA 2E2IL 1R0JA 2NVTL 3KYXA 2PYAA 2XJQA 4AYBP 1WJVA 1BE7A 4QIWP 2ZIXA 1DX8A 4LHNA 1T9OA 3PO3L 1RDVA 3HJWB 3S1NL 3PO2L 2XJSA 3K35A 1B2JA 1TWAL 1SMUA 1B2OA 4A3ML 2B63L 1FHMA 3KYWA 3MSUA 4XGHA 4AR5A 2L0ZA 3HOZL 1SMMA 3PIP1 2PMZP 4AI3A 5C4XL 1Y1VL 2LCQA 1LKPA 5JVH1 3KYYA 4YWMA 1IW7D 4TPUA 1S30A 1VZGA 5MFZA 2R7ZL 1RYQA 4AR3A 1LKOA 2MS3A 1B71A 4UY81 4AI1A 1ODHA 3J7Z1 4WFN1 1B13A 1RB9A 4BY7L 3KYUA 5IY0A 2PSMC 1NXGA 1YUXA 1P7PA 3B08B 2A68D 1IU6A 4AI2A 1FHHA 3S2HL 3PZAA 3HKZP 1NXEA 3QQCE 2J9UB 5RXNA 2JA7L 4POFA 1K83L 1PFWA 2ERJA 2A6HD 3J7Y1 3CQZL 5H1Sc 3LWRB 1PFYA 4C2M1 3HOVL 5AI3A 1IU5A 1SFOL 7RXNA 2O5JD 3RZTA 3FKIL 1BFYA 4AR4A 3S14L 4AI0A 3KYVA 4A3LL 3HOWL 2E2JL 3S1ML 1OWBA 5GAEc 1PFUA 2Y0SP 4A3GL 3RYGA 5MGNA 4Y7NL 3WWNB 3M4OL 5GAGc 1PFVA 3H9CA 4A3BL 3H3VM 3GTOL 5C44L 3GTQL 4AHZA 2WAQP 1YK4A 3GTPL 5DM61 2K2DA 1VZIA 2M4VA 1OWCA 2NVYL 3PWFA 3LWPB 4BBRL 2AUSB 1QQTA 2GMGA 3MQKB 1R9TL 3HOYL 3H0GL 1Z92B 3I4ML 2HVYC 1BQ9A 4C3JL 2B5ID 4G6BA 4A3EL 2ERSA 1H7VA 4RXNA 2H12A 5MF6A 3GTLL 2CR8A 2C6BA 4A3IL 1I3QL 2KN9A 2JI2A 2AQCA 3FDJA 2WB1P 2PVEA 3HJYB 3GTGL 3SS2A 3PIO1 3S2DL 2V0FA 2XJRA 2Z3RB 1SMWA 1QCVA 4A3FL 3LWOB 5M5XL 5GAHc 2XJUA 1IROA 2QL0A 4AHXA 3PL5A 3S15L 3NFPI 1TWFL 4U671 1BQ8A 4B8CD
chains in the Genus database with same CATH topology
4AYBP 3FKIL 1TWHL 3GTML 4QIWP 3S14L 4A93L 4A3LL 3HOWL 3HOXL 5C3EL 2E2JL 3S1ML 2Y0SP 4A3GL 3PO3L 4Y7NL 4A3KL 3M4OL 3S1NL 1WCML 2NVXL 5IP7L 1TWGL 3PO2L 5IYCL 4A3BL 3H3VM 1I6HL 2JA8L 3I4NL 4C3HL 1TWAL 5C44L 4A3JL 3GTOL 3GTQL 2B63L 4A3ML 5M3ML 1TWCL 3S16L 1I50L 3K7AL 2WAQP 3GTPL 5FJ8L 3HOZL 4X6AL 3S17L 2PMZP 5IYBL 2NVYL 4BBRL 5C4XL 1Y1VL 3S1RL 1R9TL 3HOYL 2E2HL 3H0GL 4BXXL 4A3CL 3I4ML 3GTJL 4C3JL 2YU9L 2R7ZL 4A3EL 3HOUL 5IYDL 5M3FL 2VUML 3GTLL 4BY7L 4A3IL 1I3QL 5M5WL 2WB1P 3GTGL 5M5YL 3S2DL 4BBSL 2R93L 3S2HL 5C4JL 2R92L 3HKZP 4A3FL 5FLML 5M5XL 2JA7L 2JA6L 5IP9L 4BY1L 3RZOL 4C3IL 2JA5L 4Y52L 1K83L 3S1QL 3RZDL 3CQZL 3M3YL 3S15L 3GTKL 2NVQL 1TWFL 4C2M1 3HOVL 2E2IL 1SFOL 2NVTL 1Y1WL 4A3DL
chains in the Genus database with same CATH homology


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