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


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