3S1NL

Rna polymerase ii initiation complex with a 5-nt rna (variant 2)
Total Genus 3
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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
3
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 tags Transcription/rna/dna
publication title Initiation complex structure and promoter proofreading.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 3
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2011-05-15

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 3s1nL00
3PO2L 4AYBP 4C3IL 3HOXL 2B63L 3GTML 5M3FL 3GTPL 3HOVL 4C3HL 1R9TL 3M3YL 2PMZP 2Y0SP 3HOWL 2JA8L 2JA6L 3H3VM 4BY1L 5M5XL 4C2M1 2E2JL 4A3EL 3S15L 3HOYL 2E2HL 2R93L 4A3IL 3RZOL 4X6AL 1WCML 3HKZP 1Y1VL 4A3BL 5C4JL 1TWCL 1Y1WL 3GTOL 4A3ML 3GTKL 3S16L 3S17L 2E2IL 2VUML 3CQZL 4C3JL 5C3EL 5M5WL 2JA7L 2NVYL 3PO3L 4A3FL 3GTGL 1K83L 2WB1P 1I50L 1I3QL 2WAQP 3K7AL 3H0GL 4BY7L 2NVXL 2NVTL 2NVQL 5C44L 5IP9L 3S14L 3HOUL 2R92L 3FKIL 5IYCL 3S1RL 1TWAL 1TWFL 3GTJL 3S1QL 2R7ZL 4QIWP 3GTLL 5M5YL 3S2HL 5IYBL 4A3KL 3I4NL 4BBSL 4Y52L 3GTQL 2JA5L 4BXXL 5M3ML 3S1NL 4A93L 5FJ8L 3RZDL 5IYDL 5FLML 3HOZL 5C4XL 4A3GL 1TWGL 2YU9L 4A3DL 3I4ML 5IP7L 3S2DL 1I6HL 4Y7NL 3S1ML 4A3JL 4A3LL 4BBRL 1SFOL 1TWHL 4A3CL 3M4OL
chains in the Genus database with same CATH superfamily
3PIO1 1Z92B 2RFKB 3H99A 2K2DA 2A68D 3KYWA 3M3YL 5RXNA 2CKAA 3LWVB 2Y0SP 1IROA 1E8JA 3H3VM 4C2M1 4A3EL 1RB9A 2E2HL 2JI1A 2R93L 1T9PA 3HKZP 3J7Z1 5GAGc 4AHXA 4A3BL 2MS3A 3SS2A 1VCXA 3MQKB 2E2IL 1PZXA 2VUML 1YV1A 3CQZL 2CR8A 5C3EL 3LWPB 5AI3A 1RYTA 3MSUA 3VPBE 3HAXC 3GTGL 1PFUA 4AR4A 1I50L 1FHMA 2WAQP 3K7AL 2NVXL 4ME3A 1B71A 4LHLA 1B2OA 3HOUL 1VZIA 4JAFA 1R0FA 2HR5A 3PKIA 4AR6A 1R0HA 2R7ZL 5IY0A 1RDGA 4Y52L 3GTQL 4K9FA 2PSMC 3IU3I 3J7Y1 5IYDL 2L0ZA 5C4XL 3JR7A 4A3GL 2JI2A 1TWGL 3RZ6A 1LTLA 2C6AA 2XJTA 3S2DL 4Y7NL 3S1ML 4A3JL 1R0IA 2AUSB 4U671 4A3CL 3PO2L 4GS7D 4C3IL 3HOXL 5EIOC 2PYAA 3P2AA 2V3BB 4C3HL 1R9TL 1P7PA 3QVDA 1B13A 4XXBB 3HOWL 2H12A 3NFPI 4LHNA 1QQTA 2XJPA 4AHYA 3LNLA 5MFPA 2E2JL 2A6HD 3LWRB 3PKJA 1QYBA 4A3IL 3PIP1 4AR5A 1WCML 1Y1VL 3HJWB 5C4JL 1TWCL 3HJYB 2ZIXA 1CAAA 3GTKL 1RWDA 2GMGA 1T9QA 3MPSA 2V0EA 1FHHA 4UY81 1K83L 2PVEA 1SMUA 7RXNA 2LCQA 1I3QL 1LKPA 4BY7L 2R92L 3LWQB 1F4LA 1TWAL 5MFZA 5JVG1 3PZAA 3KYVA 3I4NL 4BBSL 4BXXL 1BQ9A 5FJ8L 3RZDL 3WWNB 2J9UB 1BE7A 1CADA 2XJRA 1OWBA 3PL5A 2M4YA 3WWLA 5IP7L 2M6PA 2HVYC 2XJQA 1RDVA 1R0GA 4BBRL 1SFOL 1VZGA 4AYBP 1LKMA 2B63L 1QCVA 4AR3A 1IW7D 3GTML 1OWCA 1WJVA 3QQCE 4AI1A 3GTPL 3HOVL 1VZHA 3LWOB 4JAEA 1S2ZA 2JA8L 2JA6L 5GADc 5M5XL 4AHWA 3S15L 1ODHA 1YUZA 2B5ID 3ZG6A 3RZOL 4X6AL 1H7VA 3RZTA 2NYDA 1Y1WL 3GTOL 4A3ML 3H9CA 3S16L 3S17L 4G6BA 1SMMA 1LKOA 4AHZA 1YUXA 1B2JA 3KYUA 4A3FL 5GAHc 5GAEc 1R0JA 5EINC 5DM61 5H1Sc 1BRFA 2XJVA 2NVTL 2NVQL 5MGNA 2Z3QB 3S14L 8RXNA 2KN9A 3FKIL 1IU5A 2ERSA 3S1RL 4ZN1B 4YWLA 3GTJL 4JADA 6RXNA 2M4VA 4POFA 5M5YL 1PFYA 1NXEA 3LPEB 5IYBL 4POGA 3S1NL 4A93L 3P8BA 5FLML 1PFVA 3KYXA 3PWFA 2M6OA 2YU9L 4A3DL 3B08B 3I4ML 1I6HL 4V196 1YK4A 4A3LL 2A69D 1BFYA 3M4OL 2KKDA 5M3FL 5DM71 5MLC3 4RXNA 4AI2A 2PMZP 1T9OA 1NXGA 2XJUA 2C6BA 1S24A 5K2ME 4BY1L 4TPUA 2EY4E 1YK5A 3B0AB 4AI0A 2PPTA 3HOYL 2DSXA 2CKCA 1SMWA 1NNQA 1JYBA 2APOB 2A6ED 4TVMA 4C3JL 5M5WL 2JA7L 1IRNA 2NVYL 5MF6A 3PO3L 2JI3A 2WB1P 1S30A 2PVXA 4JAGA 4ZN3B 3H0GL 3A44A 3H9BA 3RYGA 5C44L 2AQCA 5IP9L 3K35A 1RYQA 3FDJA 5IYCL 2AYJA 1C09A 1TWFL 3S1QL 2VL6A 4QIWP 3GTLL 5AN9H 4WFN1 1PFWA 3S2HL 5JVH1 4A3KL 2O5JD 2JA5L 2ERJA 2V0FA 5M3ML 4B8CD 2QL0A 2RDVA 1BQ8A 4XGHA 2BE5D 1ZRPA 3HOZL 1IU6A 4YWMA 2Z3RB 5AI2A 2XJSA 1DX8A 3KYYA 3H97A 1DVBA 4AI3A 1TWHL 4E6YA
chains in the Genus database with same CATH topology
3PO2L 4AYBP 4C3IL 3HOXL 2B63L 3GTML 5M3FL 3GTPL 3HOVL 4C3HL 1R9TL 3M3YL 2PMZP 2Y0SP 3HOWL 2JA8L 2JA6L 3H3VM 4BY1L 5M5XL 4C2M1 2E2JL 4A3EL 3S15L 3HOYL 2E2HL 2R93L 4A3IL 3RZOL 4X6AL 1WCML 3HKZP 1Y1VL 4A3BL 5C4JL 1TWCL 1Y1WL 3GTOL 4A3ML 3GTKL 3S16L 3S17L 2E2IL 2VUML 3CQZL 4C3JL 5C3EL 5M5WL 2JA7L 2NVYL 3PO3L 4A3FL 3GTGL 1K83L 2WB1P 1I50L 1I3QL 2WAQP 3K7AL 3H0GL 4BY7L 2NVXL 2NVTL 2NVQL 5C44L 5IP9L 3S14L 3HOUL 2R92L 3FKIL 5IYCL 3S1RL 1TWAL 1TWFL 3GTJL 3S1QL 2R7ZL 4QIWP 3GTLL 5M5YL 3S2HL 5IYBL 4A3KL 3I4NL 4BBSL 4Y52L 3GTQL 2JA5L 4BXXL 5M3ML 3S1NL 4A93L 5FJ8L 3RZDL 5IYDL 5FLML 3HOZL 5C4XL 4A3GL 1TWGL 2YU9L 4A3DL 3I4ML 5IP7L 3S2DL 1I6HL 4Y7NL 3S1ML 4A3JL 4A3LL 4BBRL 1SFOL 1TWHL 4A3CL 3M4OL
chains in the Genus database with same CATH homology


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