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


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