3GTJL

Backtracked rna polymerase ii complex with 13mer 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
b'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 3gtjL00
5IP9L 4C3HL 3H0GL 2B63L 4X6AL 4C3IL 5M3FL 3CQZL 2NVQL 3M3YL 1SFOL 5M3ML 4A93L 3HOYL 4C2M1 4BY1L 1TWFL 2R7ZL 2WAQP 5IYDL 1TWGL 2E2HL 5M5XL 1R9TL 3I4ML 2Y0SP 2R92L 3GTPL 4A3DL 2PMZP 2E2IL 3GTOL 4A3ML 3HOUL 2JA8L 3S1ML 5IYCL 4QIWP 4A3BL 5C44L 3S2HL 3FKIL 3I4NL 3K7AL 4Y7NL 5C4JL 1I6HL 3HOVL 4AYBP 4BY7L 3GTLL 2WB1P 1Y1WL 2JA5L 3PO3L 5FLML 3RZDL 3S1RL 4BBSL 2R93L 4A3GL 4A3LL 3M4OL 3HOXL 2JA6L 3S1NL 3PO2L 3S14L 3GTGL 2VUML 3GTKL 3GTQL 4A3JL 3GTML 4A3IL 5FJ8L 1TWHL 1I3QL 1WCML 5IP7L 3HOZL 3S2DL 5C4XL 2NVTL 3GTJL 5M5WL 4C3JL 2NVYL 1TWCL 3S1QL 5IYBL 1I50L 4A3KL 4BBRL 2YU9L 5C3EL 1K83L 3HKZP 2NVXL 3S17L 4A3FL 3RZOL 3HOWL 3S16L 4Y52L 1TWAL 4A3CL 3H3VM 2E2JL 1Y1VL 4BXXL 2JA7L 3S15L 4A3EL 5M5YL
chains in the Genus database with same CATH superfamily
5IP9L 5GAHc 3H0GL 2M4VA 2B63L 4X6AL 2NVQL 3M3YL 1PFWA 2V0FA 5MGNA 4YWMA 2V3BB 3PKIA 3HOYL 4K9FA 3KYWA 4TPUA 1R0HA 5IYDL 1OWBA 1SMWA 2M4YA 1Z92B 4A3DL 3MPSA 3QVDA 2XJSA 4JAEA 1E8JA 8RXNA 4A3ML 4YWLA 2JA8L 1P7PA 1T9OA 1RDVA 2KKDA 4BY7L 2WB1P 1YK5A 3LPEB 2JI1A 1RYQA 1YUXA 3HOXL 1RB9A 3LWVB 3S1NL 1S30A 3PO2L 3S14L 3GTGL 3GTKL 3GTQL 2LCQA 1IRNA 2PYAA 2HVYC 3KYYA 2KN9A 1TWHL 3RYGA 3J7Z1 1IU6A 3WWNB 2XJRA 1S24A 4AR4A 2XJPA 3PKJA 4BBRL 4RXNA 1T9PA 4AR3A 1QQTA 2NVXL 3S17L 4LHNA 1LKMA 4ME3A 5MF6A 5DM61 5DM71 1NXGA 4JADA 1BQ8A 3S16L 3HJWB 2AQCA 4AI3A 1Y1VL 1R0JA 2JA7L 1IROA 3WWLA 5EINC 3PZAA 1FHMA 1LKOA 3CQZL 4AHWA 1FHHA 5AN9H 3SS2A 1PFUA 4POGA 1TWFL 3HAXC 1IW7D 4AHXA 4AR6A 1TWGL 4AHZA 2PPTA 2GMGA 2E2HL 5IY0A 2ZIXA 3I4ML 2O5JD 4UY81 2J9UB 3GTOL 6RXNA 3HOUL 1RDGA 2PSMC 3S1ML 5IYCL 4A3BL 2AUSB 3S2HL 4AI1A 3I4NL 3K7AL 1SMMA 2V0EA 5C4JL 2A69D 1Y1WL 1CAAA 3RZTA 5GAGc 2DSXA 2MS3A 2M6OA 4TVMA 5JVH1 3M4OL 2JA6L 3PIO1 4JAFA 2CR8A 2PVXA 5GADc 4A3IL 2NYDA 3ZG6A 4G6BA 1B2OA 5MLC3 1I3QL 2XJQA 3H99A 3S2DL 1H7VA 2B5ID 2EY4E 3HJYB 4C3JL 2VL6A 1YV1A 3S1QL 1VZIA 2C6AA 3P8BA 7RXNA 3LWRB 1CADA 2K2DA 3B0AB 5C3EL 4ZN1B 4JAGA 3QQCE 1BRFA 3RZOL 4XXBB 2XJTA 4A3CL 4GS7D 3S15L 2C6BA 1B2JA 1JYBA 2PVEA 1SFOL 3KYVA 1ZRPA 5M3ML 5JVG1 5MFZA 4A93L 5GAEc 4C2M1 4BY1L 2R7ZL 2WAQP 1WJVA 4AR5A 1QYBA 4LHLA 5M5XL 3IU3I 5EIOC 1B13A 2CKCA 2PMZP 2E2IL 1NXEA 1VZHA 3H9CA 3K35A 5C44L 3H97A 4Y7NL 1OWCA 4AYBP 3LWQB 1R0IA 2JA5L 2ERJA 5FLML 3RZDL 3S1RL 4BBSL 2R93L 4A3GL 5AI3A 1LTLA 4V196 2M6PA 4ZN3B 1BQ9A 4A3JL 3LWPB 1DX8A 5FJ8L 2APOB 3J7Y1 1WCML 4POFA 5IP7L 3GTJL 5M5WL 1ODHA 2CKAA 2ERSA 5AI2A 1T9QA 3MSUA 1PFYA 3RZ6A 1I50L 1LKPA 3PWFA 2L0ZA 1DVBA 4A3FL 1B71A 1TWAL 3H3VM 5K2ME 4E6YA 1R0FA 3FDJA 1VCXA 1R0GA 4C3HL 1SMUA 4AHYA 4XGHA 4C3IL 5M3FL 3LNLA 1BE7A 3MQKB 1BFYA 1C09A 3H9BA 5MFPA 4B8CD 2HR5A 1IU5A 4AI2A 1VZGA 1R9TL 2Y0SP 2R92L 3GTPL 1RYTA 2RDVA 3LWOB 2A6ED 3KYUA 2Z3RB 4QIWP 3FKIL 1QCVA 1RWDA 2JI3A 1I6HL 3HOVL 3GTLL 2XJVA 3PO3L 3P2AA 4U671 3PIP1 4A3LL 5RXNA 4WFN1 3VPBE 2VUML 3NFPI 3GTML 2AYJA 3JR7A 1PFVA 2QL0A 3PL5A 3HOZL 5C4XL 2JI2A 2RFKB 2NVTL 2H12A 2NVYL 1TWCL 3KYXA 5IYBL 4A3KL 1NNQA 2YU9L 3A44A 1K83L 1S2ZA 2XJUA 3B08B 3HKZP 1F4LA 4AI0A 2BE5D 3HOWL 1YUZA 1PZXA 5H1Sc 2A68D 4Y52L 2E2JL 1YK4A 4BXXL 2A6HD 4A3EL 2Z3QB 5M5YL
chains in the Genus database with same CATH topology
5IP9L 4C3HL 3H0GL 2B63L 4X6AL 4C3IL 5M3FL 3CQZL 2NVQL 3M3YL 1SFOL 5M3ML 4A93L 3HOYL 4C2M1 4BY1L 1TWFL 2R7ZL 2WAQP 5IYDL 1TWGL 2E2HL 5M5XL 1R9TL 3I4ML 2Y0SP 2R92L 3GTPL 4A3DL 2PMZP 2E2IL 3GTOL 4A3ML 3HOUL 2JA8L 3S1ML 5IYCL 4QIWP 4A3BL 5C44L 3S2HL 3FKIL 3I4NL 3K7AL 4Y7NL 5C4JL 1I6HL 3HOVL 4AYBP 4BY7L 3GTLL 2WB1P 1Y1WL 2JA5L 3PO3L 5FLML 3RZDL 3S1RL 4BBSL 2R93L 4A3GL 4A3LL 3M4OL 3HOXL 2JA6L 3S1NL 3PO2L 3S14L 3GTGL 2VUML 3GTKL 3GTQL 4A3JL 3GTML 4A3IL 5FJ8L 1TWHL 1I3QL 1WCML 5IP7L 3HOZL 3S2DL 5C4XL 2NVTL 3GTJL 5M5WL 4C3JL 2NVYL 1TWCL 3S1QL 5IYBL 1I50L 4A3KL 4BBRL 2YU9L 5C3EL 1K83L 3HKZP 2NVXL 3S17L 4A3FL 3RZOL 3HOWL 3S16L 4Y52L 1TWAL 4A3CL 3H3VM 2E2JL 1Y1VL 4BXXL 2JA7L 3S15L 4A3EL 5M5YL
chains in the Genus database with same CATH homology


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