3S1QL

Rna polymerase ii initiation complex with a 5-nt 3'-deoxy rna soaked with atp
Total Genus 1
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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
1
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 1
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 3s1qL00
2PMZP 5M5WL 3HOXL 3GTQL 5IP7L 2E2IL 3GTLL 5C3EL 1TWAL 2R93L 2E2JL 5M3FL 5IYBL 5C44L 5M3ML 3M4OL 3H3VM 1I6HL 4A3LL 5IYCL 2NVTL 3RZOL 3HOZL 4BY1L 2Y0SP 2JA5L 2VUML 3S1ML 1WCML 1SFOL 4BBSL 4Y7NL 3S1NL 3HOYL 3PO3L 3HKZP 2E2HL 2R7ZL 2YU9L 4A3DL 1TWCL 5IYDL 2JA7L 1TWFL 3RZDL 1TWGL 4BY7L 4QIWP 3S14L 4A3IL 3H0GL 3S1RL 5M5XL 1Y1WL 4BBRL 3GTML 3S2HL 4C3IL 3GTGL 4A3CL 3GTOL 3HOVL 4BXXL 2NVYL 4C3HL 4A3FL 5M5YL 1R9TL 3GTKL 4C2M1 2JA6L 3S16L 5FLML 4AYBP 2JA8L 3K7AL 3GTPL 2NVXL 2R92L 2WAQP 3S15L 4A3ML 4C3JL 4A3BL 5C4XL 3I4ML 3S17L 5IP9L 1Y1VL 3HOUL 2NVQL 3HOWL 4A93L 4A3KL 3S2DL 4X6AL 4Y52L 1I3QL 3I4NL 4A3GL 5C4JL 2B63L 5FJ8L 4A3EL 3CQZL 4A3JL 3M3YL 3S1QL 1I50L 1K83L 2WB1P 3GTJL 3FKIL 3PO2L 1TWHL
chains in the Genus database with same CATH superfamily
1ZRPA 2PMZP 3HOXL 5IP7L 4RXNA 1YK4A 3GTLL 1VZGA 1TWAL 3KYYA 1BRFA 5IYBL 2XJTA 1RDVA 3LWQB 4B8CD 3MQKB 3H3VM 1I6HL 1SMUA 2M4YA 4ZN1B 1P7PA 3FDJA 1NXEA 3JR7A 2Y0SP 2A68D 2V0EA 4XXBB 2LCQA 2H12A 3PZAA 2QL0A 2R7ZL 2HVYC 1TWCL 5AI2A 1C09A 2APOB 1BE7A 1YUZA 1VCXA 3H0GL 7RXNA 2V3BB 1IRNA 3GTML 5GADc 4A3CL 1S30A 1T9QA 4BXXL 2M6PA 4C3HL 4A3FL 1R9TL 3GTKL 1VZIA 1BQ9A 1IW7D 5MF6A 3HJWB 2JA6L 3A44A 3VPBE 1ODHA 4XGHA 1Z92B 4AYBP 1QYBA 2R92L 4JAEA 2B5ID 4A3ML 1F4LA 4C3JL 2A69D 4LHLA 5RXNA 2XJPA 2NVQL 2A6HD 3S2DL 1B2JA 3MSUA 3I4NL 5FJ8L 3CQZL 2JI1A 4A3JL 3S1QL 2AUSB 2WB1P 1RYTA 2V0FA 3PO2L 1TWHL 2JI2A 4ME3A 2E2IL 2KKDA 5C3EL 2E2JL 2DSXA 2GMGA 3M4OL 4JAFA 3PIO1 1R0GA 5GAHc 2NVTL 4UY81 4AI1A 1LKPA 2XJRA 2JA5L 2EY4E 2JI3A 2CKAA 1LTLA 2HR5A 1YV1A 1IU6A 1SFOL 4AR3A 3PO3L 2Z3QB 1RDGA 2C6BA 2E2HL 4JADA 2AQCA 3RYGA 5IYDL 2KN9A 2JA7L 1QCVA 4BY7L 4AR4A 5GAGc 1WJVA 2ERJA 3GTOL 3HOVL 2NVYL 2M4VA 3P8BA 1S24A 5IY0A 4AR5A 2ZIXA 5MFZA 4G6BA 5EINC 1T9OA 2JA8L 2XJQA 2NVXL 3P2AA 1B71A 1PFVA 4A3BL 3SS2A 3WWNB 5MLC3 3I4ML 3S17L 6RXNA 3RZ6A 1Y1VL 3LNLA 3PKIA 2ERSA 3LWPB 4X6AL 1BQ8A 1FHMA 1PFUA 1SMMA 5C4JL 1T9PA 3GTJL 1H7VA 3KYXA 1YK5A 4AI3A 5M5WL 3GTQL 1DX8A 4E6YA 4AHYA 1OWBA 1YUXA 3QQCE 4WFN1 5M3FL 5C44L 1R0FA 5M3ML 1PZXA 5MGNA 3NFPI 1B13A 4AI2A 4A3LL 2K2DA 3H99A 4LHNA 3RZOL 5DM61 3HOZL 4BY1L 3S1ML 1RB9A 1WCML 4BBSL 1NNQA 3S1NL 3HOYL 3IU3I 3HKZP 3B0AB 4A3DL 2O5JD 5GAEc 3RZDL 1TWGL 4QIWP 5H1Sc 3PKJA 2AYJA 3QVDA 3K35A 4BBRL 1Y1WL 4AR6A 1PFYA 4V196 3S2HL 4C3IL 3GTGL 1E8JA 5DM71 1IROA 4POGA 4U671 3H9BA 3J7Y1 1S2ZA 1NXGA 3K7AL 3GTPL 3S15L 1FHHA 5AN9H 2Z3RB 4POFA 1RYQA 5C4XL 4K9FA 3KYWA 4ZN3B 4AI0A 3HOWL 4A3KL 1I3QL 2C6AA 5EIOC 2B63L 4A3EL 2XJUA 1SMWA 1K83L 2PVXA 3FKIL 5MFPA 2PYAA 3MPSA 3HAXC 1LKMA 5JVG1 2R93L 1R0HA 3LWRB 5JVH1 2XJVA 2PVEA 1OWCA 1CAAA 1QQTA 4AHZA 1LKOA 3LWVB 3LPEB 5IYCL 1IU5A 2VL6A 2PPTA 3RZTA 2CR8A 1R0JA 2VUML 4TPUA 3ZG6A 3B08B 1B2OA 4Y7NL 3PWFA 2M6OA 2YU9L 1VZHA 3H97A 1TWFL 1JYBA 2MS3A 4A3IL 3S14L 2CKCA 4JAGA 3HJYB 3S1RL 1CADA 5M5XL 3H9CA 5AI3A 4AHWA 2RDVA 1RWDA 5M5YL 3KYVA 2XJSA 4C2M1 1R0IA 4YWLA 2L0ZA 3KYUA 8RXNA 3S16L 5FLML 2BE5D 2WAQP 2A6ED 4GS7D 3WWLA 3J7Z1 2J9UB 3PL5A 4YWMA 2NYDA 5IP9L 3HOUL 4TVMA 3LWOB 2PSMC 4A93L 1DVBA 4Y52L 5K2ME 4AHXA 4A3GL 1BFYA 3M3YL 2RFKB 1I50L 1PFWA 3PIP1
chains in the Genus database with same CATH topology
2PMZP 5M5WL 3HOXL 3GTQL 5IP7L 2E2IL 3GTLL 5C3EL 1TWAL 2R93L 2E2JL 5M3FL 5IYBL 5C44L 5M3ML 3M4OL 3H3VM 1I6HL 4A3LL 5IYCL 2NVTL 3RZOL 3HOZL 4BY1L 2Y0SP 2JA5L 2VUML 3S1ML 1WCML 1SFOL 4BBSL 4Y7NL 3S1NL 3HOYL 3PO3L 3HKZP 2E2HL 2R7ZL 2YU9L 4A3DL 1TWCL 5IYDL 2JA7L 1TWFL 3RZDL 1TWGL 4BY7L 4QIWP 3S14L 4A3IL 3H0GL 3S1RL 5M5XL 1Y1WL 4BBRL 3GTML 3S2HL 4C3IL 3GTGL 4A3CL 3GTOL 3HOVL 4BXXL 2NVYL 4C3HL 4A3FL 5M5YL 1R9TL 3GTKL 4C2M1 2JA6L 3S16L 5FLML 4AYBP 2JA8L 3K7AL 3GTPL 2NVXL 2R92L 2WAQP 3S15L 4A3ML 4C3JL 4A3BL 5C4XL 3I4ML 3S17L 5IP9L 1Y1VL 3HOUL 2NVQL 3HOWL 4A93L 4A3KL 3S2DL 4X6AL 4Y52L 1I3QL 3I4NL 4A3GL 5C4JL 2B63L 5FJ8L 4A3EL 3CQZL 4A3JL 3M3YL 3S1QL 1I50L 1K83L 2WB1P 3GTJL 3FKIL 3PO2L 1TWHL
chains in the Genus database with same CATH homology


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