3S2HL

Rna polymerase ii initiation complex with a 6-nt rna containing a 2[prime]-iodo atp
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 3s2hL00
4QIWP 5IP9L 2WAQP 3RZDL 2E2HL 2PMZP 3HOWL 5FLML 1I6HL 3GTPL 3S15L 4A3JL 2NVXL 4A3IL 5C3EL 2B63L 3S2HL 4AYBP 2VUML 3GTKL 3RZOL 4C3HL 3GTGL 3HOZL 3S17L 2R92L 3HKZP 1TWAL 4A3DL 1WCML 1Y1VL 3I4ML 3GTOL 3HOXL 2WB1P 3GTML 3S14L 4A3GL 5C44L 2R7ZL 4C3IL 4X6AL 4A3KL 3HOVL 5C4XL 5FJ8L 3GTJL 5M5XL 2NVYL 1TWFL 3I4NL 3M3YL 5M5WL 4A3ML 1Y1WL 3GTQL 3H3VM 3S1NL 4Y7NL 2YU9L 5M5YL 2JA7L 3S16L 3GTLL 5M3ML 2R93L 3PO2L 1I3QL 4Y52L 2E2JL 1TWHL 4BY7L 5C4JL 4A3LL 4C2M1 4BBSL 2NVTL 5IP7L 3PO3L 4A3CL 1K83L 2E2IL 3FKIL 3S2DL 4A3BL 3K7AL 3HOYL 1TWGL 1TWCL 3S1QL 3CQZL 1R9TL 5IYCL 2JA6L 2JA8L 3S1ML 4BXXL 4BBRL 3H0GL 3S1RL 3M4OL 2Y0SP 5M3FL 1SFOL 4A3EL 4A93L 2NVQL 4A3FL 4BY1L 4C3JL 2JA5L 3HOUL 5IYBL 1I50L 5IYDL
chains in the Genus database with same CATH superfamily
2XJTA 3KYWA 2WAQP 2E2HL 2PVEA 5FLML 1RDGA 2A68D 2B63L 3S2HL 5JVG1 3GTKL 3RZOL 3LPEB 3RYGA 3A44A 1B2JA 1TWAL 1WCML 1Y1VL 3K35A 3GTOL 3HOXL 4UY81 2MS3A 3S14L 5MFZA 1CADA 2R7ZL 3KYVA 2KN9A 1BQ9A 3IU3I 5MFPA 5DM71 1T9OA 1T9QA 3M3YL 4E6YA 2B5ID 3QVDA 2RDVA 1SMUA 1YUXA 1LKMA 1JYBA 1FHHA 2JI1A 3ZG6A 3S16L 2AYJA 3GTLL 3NFPI 1I3QL 2XJUA 1TWHL 3LWQB 2V0EA 2C6BA 4A3CL 1YK4A 1SMMA 3K7AL 3S1QL 2CKAA 3S1ML 3KYUA 1RB9A 2Y0SP 4G6BA 4POGA 4JAEA 3PKJA 1IROA 3LNLA 1R0IA 4AHYA 5AI3A 2AQCA 2O5JD 2XJRA 6RXNA 1YV1A 3PZAA 1PFYA 1IRNA 5AN9H 1LTLA 4QIWP 3H9CA 5EIOC 3HJYB 2GMGA 2PMZP 1PFWA 3HOWL 5MLC3 3RZTA 4YWMA 1IW7D 3GTPL 4A3IL 4K9FA 4TPUA 3WWLA 4C3HL 4LHNA 3S17L 1LKOA 1PZXA 2V0FA 5GAGc 1IU6A 3HKZP 2RFKB 4A3DL 2CKCA 2QL0A 3GTML 3H99A 5C44L 3KYYA 1QCVA 5MGNA 4X6AL 3HOVL 1OWCA 1NNQA 4AI3A 5M5XL 1P7PA 2PYAA 4RXNA 4GS7D 1VZGA 3H3VM 3PKIA 1B13A 1WJVA 3PWFA 4AR6A 2XJPA 1ZRPA 3RZ6A 4Y7NL 1B2OA 2AUSB 2A6ED 2PSMC 2YU9L 5M5YL 5M3ML 3MQKB 3P2AA 5RXNA 4BY7L 5C4JL 4C2M1 1R0GA 1BRFA 2E2IL 3FKIL 2C6AA 5H1Sc 3HOYL 1TWGL 3LWPB 1QQTA 3CQZL 5IYCL 2JA6L 2JA8L 2V3BB 4V196 3M4OL 3HJWB 4U671 4JAGA 5DM61 4A93L 2NVQL 4A3FL 2H12A 2ERJA 2K2DA 3B08B 1I50L 2JI3A 5GADc 5IYDL 5EINC 5IP9L 3RZDL 3PL5A 4XXBB 4ME3A 5MF6A 1H7VA 2CR8A 3S15L 4A3JL 1NXEA 3KYXA 3LWRB 2DSXA 2BE5D 2M6OA 2XJVA 1DX8A 3H97A 3GTGL 3HOZL 2R92L 4AHXA 1T9PA 1VCXA 4A3GL 4LHLA 1R0FA 5C4XL 5FJ8L 2M4YA 2NVYL 1TWFL 3P8BA 3I4NL 1IU5A 3WWNB 2KKDA 5M5WL 4A3ML 1Y1WL 2M4VA 1BQ8A 3S1NL 1DVBA 3J7Z1 2JA7L 2R93L 4Y52L 3SS2A 2E2JL 1RYQA 3PIO1 4BBSL 4XGHA 2PVXA 5IP7L 3VPBE 1K83L 1SMWA 1RWDA 4YWLA 4A3BL 2A69D 5GAHc 3PIP1 1QYBA 1F4LA 4BBRL 2ERSA 4JAFA 3B0AB 3S1RL 2HVYC 4POFA 1FHMA 2APOB 4AR5A 1Z92B 1YUZA 3HAXC 4AI2A 1E8JA 8RXNA 4BY1L 2JA5L 3H9BA 5AI2A 2PPTA 2NYDA 5IYBL 4JADA 5GAEc 2JI2A 4AI0A 1BE7A 3LWVB 1LKPA 3LWOB 1I6HL 1YK5A 2NVXL 5C3EL 1C09A 2J9UB 3MPSA 4AYBP 1RYTA 2Z3QB 2VUML 1BFYA 2VL6A 2XJSA 7RXNA 3I4ML 2WB1P 1NXGA 3MSUA 4C3IL 4A3KL 2ZIXA 3GTJL 2M6PA 5IY0A 4AR3A 1VZIA 2Z3RB 1S30A 4AHZA 2L0ZA 3GTQL 1VZHA 1S2ZA 3QQCE 3FDJA 2XJQA 1OWBA 1PFVA 5JVH1 3PO2L 4WFN1 1ODHA 3JR7A 4TVMA 4A3LL 2NVTL 1S24A 3PO3L 4ZN1B 1R0HA 4AHWA 3S2DL 5K2ME 2LCQA 4AR4A 1B71A 1TWCL 1RDVA 1CAAA 1R9TL 4B8CD 4BXXL 4ZN3B 1R0JA 3J7Y1 3H0GL 2HR5A 5M3FL 1SFOL 4A3EL 2A6HD 4C3JL 3HOUL 2EY4E 4AI1A 1PFUA
chains in the Genus database with same CATH topology
4QIWP 5IP9L 2WAQP 3RZDL 2E2HL 2PMZP 3HOWL 5FLML 1I6HL 3GTPL 3S15L 4A3JL 2NVXL 4A3IL 5C3EL 2B63L 3S2HL 4AYBP 2VUML 3GTKL 3RZOL 4C3HL 3GTGL 3HOZL 3S17L 2R92L 3HKZP 1TWAL 4A3DL 1WCML 1Y1VL 3I4ML 3GTOL 3HOXL 2WB1P 3GTML 3S14L 4A3GL 5C44L 2R7ZL 4C3IL 4X6AL 4A3KL 3HOVL 5C4XL 5FJ8L 3GTJL 5M5XL 2NVYL 1TWFL 3I4NL 3M3YL 5M5WL 4A3ML 1Y1WL 3GTQL 3H3VM 3S1NL 4Y7NL 2YU9L 5M5YL 2JA7L 3S16L 3GTLL 5M3ML 2R93L 3PO2L 1I3QL 4Y52L 2E2JL 1TWHL 4BY7L 5C4JL 4A3LL 4C2M1 4BBSL 2NVTL 5IP7L 3PO3L 4A3CL 1K83L 2E2IL 3FKIL 3S2DL 4A3BL 3K7AL 3HOYL 1TWGL 1TWCL 3S1QL 3CQZL 1R9TL 5IYCL 2JA6L 2JA8L 3S1ML 4BXXL 4BBRL 3H0GL 3S1RL 3M4OL 2Y0SP 5M3FL 1SFOL 4A3EL 4A93L 2NVQL 4A3FL 4BY1L 4C3JL 2JA5L 3HOUL 5IYBL 1I50L 5IYDL
chains in the Genus database with same CATH homology


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