3S1ML

Rna polymerase ii initiation complex with a 5-nt rna (variant 1)
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 Initiation complex structure and promoter proofreading.
pubmed doi rcsb
molecule tags Transcription/rna/dna
total genus 2
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 3s1mL00
3I4ML 2NVXL 1TWFL 2R92L 3HOXL 2VUML 5IP7L 4C2M1 3HOWL 3HOYL 4A3FL 4A3IL 1R9TL 3H0GL 3S2DL 5M3ML 1I6HL 1TWGL 3S15L 4C3IL 3HOUL 4QIWP 1TWCL 3RZDL 3S1ML 2JA8L 3H3VM 5C44L 5M5YL 4A3BL 5IP9L 1I50L 2E2IL 3GTLL 4A3EL 3M4OL 5C4XL 1WCML 3S14L 2JA6L 2R93L 3GTGL 5C3EL 2NVQL 4A3KL 2R7ZL 1SFOL 3HOZL 1Y1VL 3S1RL 2NVTL 3GTPL 4A3GL 2PMZP 4A3JL 5IYCL 3I4NL 2B63L 4A3DL 5M5XL 4BY1L 2JA5L 3S16L 3S17L 4Y52L 3S1QL 2JA7L 3GTOL 3CQZL 1I3QL 3GTJL 4A3CL 4C3HL 3FKIL 3S2HL 5C4JL 5M5WL 5IYBL 1TWHL 3HKZP 5IYDL 1K83L 5M3FL 5FLML 2E2JL 4Y7NL 4AYBP 3M3YL 5FJ8L 1TWAL 3PO3L 4C3JL 2WB1P 3S1NL 3PO2L 1Y1WL 4A3ML 3HOVL 4BXXL 2NVYL 3GTQL 4BBRL 2WAQP 3K7AL 2YU9L 4A3LL 2E2HL 3RZOL 4X6AL 2Y0SP 4BBSL 4A93L 4BY7L 3GTKL 3GTML
chains in the Genus database with same CATH superfamily
1NNQA 4AI3A 1QYBA 2R92L 1H7VA 3HOXL 3LWVB 3HOYL 1T9OA 4A3IL 3H0GL 3S2DL 1IU5A 5M3ML 2M6OA 1TWGL 3S15L 4C3IL 1YUXA 2APOB 5M5YL 5MLC3 3PL5A 1I50L 3PKJA 2DSXA 4TVMA 1BFYA 3QQCE 3HJYB 4A3KL 2MS3A 1PFWA 4AHZA 2XJTA 3H99A 1Y1VL 3S1RL 1SMMA 2V0EA 3S16L 3S1QL 1RB9A 3GTOL 3CQZL 1Z92B 2XJSA 1BRFA 3HAXC 5IY0A 1RDGA 3A44A 1PFYA 5IYBL 1DVBA 3P8BA 3MPSA 3KYYA 5JVH1 1IRNA 5FJ8L 1TWAL 3PO3L 3JR7A 3LWOB 6RXNA 2CKAA 4A3ML 3H97A 2V3BB 3ZG6A 1LKMA 1B13A 4A3LL 2E2HL 4X6AL 2Y0SP 4A93L 1FHMA 3GTKL 1S2ZA 2M6PA 4V196 4YWLA 2XJVA 2V0FA 2XJUA 1R0JA 3MQKB 1R9TL 3PKIA 3HOUL 4AI0A 2JA8L 1YK4A 5DM61 1CAAA 4AR6A 2KN9A 3P2AA 2JI3A 2E2IL 2C6AA 3M4OL 1WCML 4AR5A 2R93L 1VZGA 5MFPA 4AHXA 1ODHA 2NYDA 4G6BA 4A3GL 2PVXA 2PMZP 1VCXA 3J7Z1 4ZN3B 3I4NL 4GS7D 5M5XL 4B8CD 3WWNB 1WJVA 1SMUA 4ME3A 2RDVA 1IU6A 4JAFA 2LCQA 3VPBE 2QL0A 5MF6A 2H12A 2J9UB 5EINC 1RYQA 3FKIL 1R0HA 5M5WL 1LTLA 3SS2A 1TWHL 4JADA 3MSUA 4Y7NL 4C3JL 5JVG1 2WB1P 5GADc 1Y1WL 4POGA 1T9QA 3PWFA 1PZXA 1B2OA 3HOVL 1T9PA 4UY81 3KYVA 4BBRL 2EY4E 3RZOL 3KYXA 4BBSL 3B08B 4K9FA 3B0AB 5GAHc 2CKCA 4C2M1 3HOWL 5RXNA 4TPUA 2A6ED 1I6HL 1S24A 4XXBB 1PFUA 4YWMA 3KYUA 4QIWP 1TWCL 3RZDL 3S1ML 2HR5A 4RXNA 5GAEc 2XJQA 4A3BL 5IP9L 7RXNA 1PFVA 3GTLL 4JAGA 2ERSA 1FHHA 8RXNA 2ERJA 2JA6L 3LWQB 5C3EL 2NVQL 3PIO1 1OWBA 1SFOL 2A68D 2NVTL 2C6BA 5K2ME 4POFA 2M4YA 4A3JL 4LHNA 2B63L 4BY1L 4ZN1B 1BE7A 1R0FA 4Y52L 3LWPB 1VZIA 2JA7L 5H1Sc 4AR4A 4C3HL 2L0ZA 3RZ6A 3RYGA 2PYAA 5AN9H 2AQCA 1YUZA 3WWLA 5IYDL 1LKPA 1B2JA 1QCVA 1K83L 5FLML 5GAGc 2E2JL 5MFZA 3M3YL 4AI2A 3IU3I 3H9BA 1R0GA 3S1NL 4JAEA 4BXXL 1IW7D 2NVYL 3GTQL 2JI2A 1F4LA 3K35A 1B71A 1C09A 2WAQP 3LPEB 1JYBA 1RDVA 1VZHA 2JI1A 2O5JD 2AYJA 3GTML 1NXGA 3I4ML 2NVXL 3J7Y1 1TWFL 3FDJA 2GMGA 1E8JA 1OWCA 1QQTA 2VUML 5IP7L 3RZTA 4A3FL 1DX8A 4E6YA 1ZRPA 2PVEA 4AHYA 5MGNA 4WFN1 3H3VM 3H9CA 2AUSB 3KYWA 5C44L 1YK5A 1LKOA 3NFPI 4A3EL 5C4XL 2B5ID 3S14L 3GTGL 1RYTA 2PPTA 2R7ZL 2M4VA 4AI1A 2RFKB 3LWRB 3HJWB 3HOZL 2A6HD 3GTPL 5EIOC 1BQ8A 3QVDA 5IYCL 2KKDA 4A3DL 3LNLA 1SMWA 2JA5L 3S17L 1BQ9A 2Z3QB 3PIP1 5AI2A 5AI3A 2HVYC 4U671 1CADA 1I3QL 3GTJL 2VL6A 1P7PA 4A3CL 1YV1A 3S2HL 5C4JL 2ZIXA 3HKZP 1IROA 5M3FL 2A69D 2XJRA 1NXEA 2K2DA 4AYBP 2PSMC 3PO2L 4LHLA 1R0IA 3PZAA 2CR8A 2BE5D 1RWDA 5DM71 4AHWA 2XJPA 2YU9L 3K7AL 1S30A 2Z3RB 4XGHA 4BY7L 4AR3A
chains in the Genus database with same CATH topology
3I4ML 2NVXL 1TWFL 2R92L 3HOXL 2VUML 5IP7L 4C2M1 3HOWL 3HOYL 4A3FL 4A3IL 1R9TL 3H0GL 3S2DL 5M3ML 1I6HL 1TWGL 3S15L 4C3IL 3HOUL 4QIWP 1TWCL 3RZDL 3S1ML 2JA8L 3H3VM 5C44L 5M5YL 4A3BL 5IP9L 1I50L 2E2IL 3GTLL 4A3EL 3M4OL 5C4XL 1WCML 3S14L 2JA6L 2R93L 3GTGL 5C3EL 2NVQL 4A3KL 2R7ZL 1SFOL 3HOZL 1Y1VL 3S1RL 2NVTL 3GTPL 4A3GL 2PMZP 4A3JL 5IYCL 3I4NL 2B63L 4A3DL 5M5XL 4BY1L 2JA5L 3S16L 3S17L 4Y52L 3S1QL 2JA7L 3GTOL 3CQZL 1I3QL 3GTJL 4A3CL 4C3HL 3FKIL 3S2HL 5C4JL 5M5WL 5IYBL 1TWHL 3HKZP 5IYDL 1K83L 5M3FL 5FLML 2E2JL 4Y7NL 4AYBP 3M3YL 5FJ8L 1TWAL 3PO3L 4C3JL 2WB1P 3S1NL 3PO2L 1Y1WL 4A3ML 3HOVL 4BXXL 2NVYL 3GTQL 4BBRL 2WAQP 3K7AL 2YU9L 4A3LL 2E2HL 3RZOL 4X6AL 2Y0SP 4BBSL 4A93L 4BY7L 3GTKL 3GTML
chains in the Genus database with same CATH homology


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