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


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