3S2DL

Rna polymerase ii initiation complex with a 5-nt rna containing a 5br-u
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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publication title Initiation complex structure and promoter proofreading.
pubmed doi rcsb
molecule keywords DNA-directed RNA polymerase II subunit RPB1
molecule tags Transcription/rna/dna
total genus 2
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2011-05-16

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 3s2dL00
5IYBL 4X6AL 2E2JL 2JA5L 5IYCL 2E2IL 2JA8L 4A3FL 3GTKL 1I50L 2R93L 5C3EL 2JA6L 3H3VM 3GTML 4BBSL 4BXXL 1TWGL 4A3ML 4C3HL 1TWFL 2B63L 1TWHL 3S14L 5FLML 3I4NL 3RZDL 1Y1WL 1R9TL 3RZOL 3GTJL 2NVTL 3S1RL 4A3DL 5IP7L 1I3QL 3GTOL 1TWAL 4A3BL 4C2M1 4Y52L 4C3JL 3PO3L 4A3EL 4BY1L 2WAQP 3GTGL 2VUML 3GTPL 5M3ML 2PMZP 5C4JL 5M5XL 1I6HL 5IYDL 3S2HL 2NVXL 5C4XL 3CQZL 3S2DL 2WB1P 3HOZL 1Y1VL 4AYBP 3S1NL 3HOYL 3PO2L 3S1QL 3FKIL 5M3FL 4A3KL 2R7ZL 2YU9L 1SFOL 4QIWP 2JA7L 4A3GL 2E2HL 4A93L 3HOXL 4C3IL 4BY7L 3S16L 4A3CL 3S17L 3GTQL 3HKZP 5C44L 4A3LL 5M5YL 3M3YL 2Y0SP 3I4ML 4A3JL 3S15L 3H0GL 3HOUL 2NVYL 4Y7NL 5M5WL 3HOVL 3GTLL 3S1ML 3HOWL 5IP9L 3M4OL 4BBRL 3K7AL 4A3IL 1K83L 2NVQL 2R92L 1TWCL 1WCML 5FJ8L
chains in the Genus database with same CATH superfamily
4V196 2HVYC 2E2JL 2JA5L 1BQ8A 2XJVA 1WJVA 1I50L 5GAHc 2RDVA 3GTML 4BBSL 4AHWA 3NFPI 2JI1A 4C3HL 1T9OA 2B63L 3LWPB 1YUXA 4AHXA 2KKDA 3PWFA 4ZN3B 4AR3A 3S1RL 3GTOL 1TWAL 2H12A 3H9CA 1Z92B 3PO3L 3B08B 2VUML 2K2DA 5C4JL 1I6HL 5IYDL 3CQZL 5GADc 3S2DL 4AYBP 4AI0A 3PO2L 3S1QL 4A3KL 2R7ZL 1CADA 3KYXA 4QIWP 2XJRA 2E2HL 2O5JD 2C6AA 2APOB 3PZAA 1NXGA 2A69D 3LWRB 5C44L 3H99A 1BE7A 4A3LL 2XJUA 1S24A 3I4ML 2V0FA 2PPTA 3S15L 2PVXA 3PKIA 3H0GL 1YK5A 2NVYL 3QQCE 2AUSB 4JAEA 1B71A 4ZN1B 3HOVL 3HOWL 5JVH1 4RXNA 4A3IL 4XXBB 2BE5D 1SMMA 1SMWA 1QCVA 2XJTA 3RYGA 1F4LA 5IYBL 3MSUA 4AR4A 2ZIXA 2A6ED 5IYCL 2JA8L 2Z3RB 3GTKL 2R93L 5C3EL 4UY81 4BXXL 1TWGL 3FDJA 1R0IA 1TWFL 2GMGA 4AHZA 3J7Z1 1RDVA 3I4NL 5MFPA 3RZOL 3GTJL 3PL5A 3PIP1 1VZGA 6RXNA 5EINC 4G6BA 4C3JL 4AI2A 1ZRPA 4BY1L 3GTGL 1FHMA 4POGA 5GAEc 1B2OA 1IU5A 1E8JA 3S2HL 3K35A 2WB1P 1P7PA 1BRFA 2M6OA 1PZXA 2MS3A 3MQKB 1IW7D 2JI3A 2C6BA 5MFZA 3FKIL 2YU9L 1FHHA 1R0FA 1SFOL 1PFWA 2M4VA 3KYWA 1BFYA 5IY0A 4WFN1 1YUZA 4A3CL 1JYBA 3SS2A 3P8BA 2V0EA 2J9UB 4GS7D 1C09A 5MGNA 3M3YL 4A3JL 4TPUA 3P2AA 3HOUL 2PVEA 4AR5A 3HJWB 3S1ML 1LKPA 1DX8A 4XGHA 1VCXA 3M4OL 5DM61 1T9PA 1K83L 4AI1A 2XJQA 3ZG6A 1OWCA 2R92L 3RZTA 1TWCL 3HAXC 3IU3I 1RWDA 3H97A 3RZ6A 2LCQA 1RYQA 4YWLA 2AQCA 2CR8A 2JI2A 2M4YA 1B2JA 1S2ZA 2ERSA 3H3VM 1RDGA 1SMUA 2Z3QB 4A3ML 1RYTA 3S14L 1NXEA 3RZDL 1Y1WL 1R0GA 5MLC3 1R9TL 1PFVA 1IROA 3WWNB 2A68D 4A3DL 2CKCA 4A3BL 3B0AB 1YV1A 4A3EL 1CAAA 2WAQP 3GTPL 1QQTA 5M5XL 4AHYA 1S30A 2KN9A 1VZIA 2CKAA 3HOZL 4ME3A 4POFA 3HOYL 3PKJA 5DM71 3KYVA 5M3FL 1ODHA 4A3GL 1LKMA 5GAGc 4C3IL 3HOXL 4BY7L 4B8CD 1OWBA 1B13A 3S17L 3GTQL 2QL0A 3HKZP 2V3BB 4TVMA 2M6PA 2Y0SP 1T9QA 4Y7NL 2VL6A 3GTLL 5IP9L 5AI3A 3KYUA 3K7AL 1R0HA 5JVG1 3HJYB 2NVQL 1WCML 5MF6A 3PIO1 4X6AL 4JAGA 2E2IL 4YWMA 4AI3A 4A3FL 5EIOC 3JR7A 3J7Y1 2PSMC 4E6YA 2JA6L 5H1Sc 3LWQB 3KYYA 1PFUA 1R0JA 3LWVB 1DVBA 2L0ZA 1IRNA 1TWHL 5FLML 2DSXA 8RXNA 1YK4A 3H9BA 1LKOA 3A44A 2NVTL 1RB9A 5IP7L 1I3QL 4C2M1 1BQ9A 1VZHA 4Y52L 3MPSA 3QVDA 4U671 5M3ML 2PMZP 1QYBA 2NVXL 5C4XL 1Y1VL 4K9FA 3S1NL 4AR6A 3LNLA 5AI2A 2EY4E 2HR5A 1LTLA 2JA7L 4LHLA 2PYAA 4A93L 3LPEB 3S16L 4JAFA 3LWOB 2A6HD 1H7VA 1PFYA 1IU6A 5M5YL 2AYJA 5AN9H 4JADA 2ERJA 2RFKB 5M5WL 2NYDA 2XJPA 1NNQA 4LHNA 4BBRL 5K2ME 7RXNA 2B5ID 5RXNA 3VPBE 5FJ8L 2XJSA 3WWLA
chains in the Genus database with same CATH topology
5IYBL 4X6AL 2E2JL 2JA5L 5IYCL 2E2IL 2JA8L 4A3FL 3GTKL 1I50L 2R93L 5C3EL 2JA6L 3H3VM 3GTML 4BBSL 4BXXL 1TWGL 4A3ML 4C3HL 1TWFL 2B63L 1TWHL 3S14L 5FLML 3I4NL 3RZDL 1Y1WL 1R9TL 3RZOL 3GTJL 2NVTL 3S1RL 4A3DL 5IP7L 1I3QL 3GTOL 1TWAL 4A3BL 4C2M1 4Y52L 4C3JL 3PO3L 4A3EL 4BY1L 2WAQP 3GTGL 2VUML 3GTPL 5M3ML 2PMZP 5C4JL 5M5XL 1I6HL 5IYDL 3S2HL 2NVXL 5C4XL 3CQZL 3S2DL 2WB1P 3HOZL 1Y1VL 4AYBP 3S1NL 3HOYL 3PO2L 3S1QL 3FKIL 5M3FL 4A3KL 2R7ZL 2YU9L 1SFOL 4QIWP 2JA7L 4A3GL 2E2HL 4A93L 3HOXL 4C3IL 4BY7L 3S16L 4A3CL 3S17L 3GTQL 3HKZP 5C44L 4A3LL 5M5YL 3M3YL 2Y0SP 3I4ML 4A3JL 3S15L 3H0GL 3HOUL 2NVYL 4Y7NL 5M5WL 3HOVL 3GTLL 3S1ML 3HOWL 5IP9L 3M4OL 4BBRL 3K7AL 4A3IL 1K83L 2NVQL 2R92L 1TWCL 1WCML 5FJ8L
chains in the Genus database with same CATH homology


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