4A3CL

Rna polymerase ii initial transcribing complex with a 5nt dna-rna hybrid
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 Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
molecule tags Transcription
total genus 1
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2011-09-30

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 4a3cL00
4Y52L 2YU9L 1TWAL 2E2HL 3GTJL 3GTOL 4AYBP 3HOYL 4A3LL 3GTGL 2PMZP 3GTKL 5IYBL 2R7ZL 3PO2L 3S1NL 1TWHL 3HOUL 3S1RL 2JA8L 2B63L 3RZDL 4A3GL 4BY1L 1WCML 3S1ML 1K83L 2WAQP 2E2JL 5IYDL 4QIWP 4C3IL 4BBRL 2JA5L 4A93L 3GTQL 4BBSL 2NVTL 2Y0SP 4A3IL 3HOZL 3S2DL 4A3JL 5M5XL 5IYCL 5FLML 2JA6L 4BXXL 5C4JL 3S16L 3GTML 3S17L 3S14L 2R93L 1TWCL 4BY7L 3RZOL 3S2HL 1Y1WL 5M5YL 1I6HL 5C44L 3PO3L 4C2M1 3H3VM 4A3DL 2WB1P 4A3EL 3S1QL 1SFOL 5FJ8L 3M4OL 1I50L 4X6AL 3I4NL 4A3FL 3HOXL 4C3JL 1TWGL 4C3HL 3FKIL 3S15L 3GTPL 2JA7L 2NVQL 3M3YL 5M3ML 1R9TL 3K7AL 5M5WL 1Y1VL 4A3CL 3HOWL 2VUML 3GTLL 5M3FL 3HKZP 4A3KL 5C3EL 2R92L 5C4XL 4Y7NL 4A3BL 3CQZL 4A3ML 2E2IL 3HOVL 3I4ML 2NVYL 3H0GL 5IP9L 5IP7L 2NVXL 1I3QL 1TWFL
chains in the Genus database with same CATH superfamily
4JAGA 3VPBE 3KYUA 2YU9L 1PFVA 1TWAL 3LNLA 2V3BB 2JI1A 2PYAA 3PKIA 4JADA 5IYBL 1RB9A 3H99A 1T9QA 1TWHL 1YK4A 3HOUL 3H9CA 5MLC3 3RZDL 4A3GL 4BY1L 3K35A 4WFN1 2CKCA 1NXGA 1R0HA 2JA5L 1PFYA 2XJSA 7RXNA 2XJUA 6RXNA 4U671 1VCXA 1R0IA 1I3QL 4BXXL 1IU6A 3KYYA 2R93L 3KYXA 3RZOL 1NXEA 1DX8A 5DM61 2CKAA 4C2M1 3H3VM 3NFPI 3S1QL 5FJ8L 1I50L 3P8BA 2ERSA 1BE7A 2H12A 2L0ZA 3MSUA 1B71A 5M3ML 1S2ZA 1LKPA 2XJVA 5M5WL 1RWDA 4E6YA 5AN9H 5MGNA 3GTLL 1Z92B 4Y7NL 3RZ6A 4A3BL 4AI2A 1WJVA 4POFA 1YUZA 1PFWA 3ZG6A 5IP9L 5GAEc 5MFPA 2V0EA 4LHLA 3J7Z1 3GTJL 3HOYL 2C6AA 3HJYB 1IW7D 4XGHA 1F4LA 2PMZP 5GAHc 1CADA 2R7ZL 3S1NL 5EINC 3JR7A 3MQKB 1WCML 1RYTA 5K2ME 4ZN1B 1K83L 2WAQP 2C6BA 5GAGc 5IYDL 4C3IL 1QCVA 2PVEA 3QVDA 3IU3I 4A3IL 1E8JA 4K9FA 3PWFA 2JI2A 5IYCL 1ODHA 5DM71 3FDJA 2XJPA 2JA6L 3LPEB 3S16L 2HR5A 2J9UB 3GTML 3S17L 2AQCA 1OWCA 4JAFA 1R0FA 1IU5A 4BY7L 2DSXA 1R0GA 4AHZA 5MF6A 1FHHA 4TPUA 3J7Y1 1B2JA 1ZRPA 3M4OL 4RXNA 4X6AL 3I4NL 4A3FL 5AI3A 2MS3A 2Z3RB 2RDVA 1DVBA 3FKIL 5JVH1 8RXNA 2M4YA 1R9TL 3K7AL 4TVMA 2VL6A 1R0JA 3HOWL 2VUML 4G6BA 1QYBA 2R92L 5C4XL 4AR6A 5H1Sc 4UY81 3CQZL 2XJQA 3I4ML 2NVYL 4ZN3B 2A68D 3PL5A 3P2AA 1SMMA 4Y52L 3GTOL 2HVYC 4AYBP 1FHMA 5RXNA 3GTGL 2EY4E 4AHXA 3PO2L 3B08B 1NNQA 2B63L 2JA8L 4AR4A 3S1ML 5IY0A 1YK5A 1BRFA 3H9BA 1C09A 1LTLA 4B8CD 2A69D 2M6PA 4BBRL 3PIP1 3GTQL 4ME3A 4A3JL 5M5XL 3SS2A 2GMGA 5C4JL 3S14L 1SMUA 1TWCL 2LCQA 4AR5A 2XJTA 2KN9A 5C44L 1PFUA 3PO3L 4A3DL 4A3EL 1SFOL 2ZIXA 3HJWB 2NYDA 3HOXL 4C3JL 3MPSA 4C3HL 3S15L 1BQ9A 3GTPL 2JA7L 1BFYA 1Y1VL 2ERJA 2M6OA 3PZAA 1OWBA 5M3FL 3HKZP 5C3EL 1IRNA 3WWNB 5GADc 2E2IL 1JYBA 3A44A 5AI2A 3H0GL 5IP7L 4YWMA 2AYJA 1TWFL 2AUSB 2PPTA 4AHYA 2E2HL 4GS7D 1YUXA 2XJRA 4A3LL 1LKMA 2KKDA 1P7PA 4V196 3PIO1 3GTKL 2K2DA 3PKJA 3HAXC 2B5ID 2V0FA 1H7VA 3S1RL 1RYQA 1RDVA 3KYWA 2Z3QB 2E2JL 1IROA 5JVG1 4QIWP 1T9OA 4POGA 3H97A 4A93L 4JAEA 4BBSL 1LKOA 2NVTL 2Y0SP 1VZHA 3RZTA 4LHNA 3HOZL 3LWPB 3S2DL 3RYGA 1RDGA 5FLML 4AR3A 2M4VA 3LWVB 4AI1A 1SMWA 3S2HL 1Y1WL 1I6HL 2PSMC 5M5YL 1CAAA 2RFKB 1T9PA 3QQCE 2WB1P 3LWOB 1QQTA 1YV1A 2QL0A 3LWRB 2PVXA 1TWGL 1VZIA 2JI3A 3WWLA 2NVQL 3M3YL 2O5JD 2BE5D 1PZXA 2APOB 1B2OA 1VZGA 4XXBB 4A3CL 4AHWA 1B13A 3B0AB 5EIOC 4A3KL 4AI0A 1S30A 5MFZA 1BQ8A 2A6HD 4AI3A 3KYVA 4A3ML 3LWQB 3HOVL 2CR8A 1S24A 4YWLA 2NVXL 2A6ED
chains in the Genus database with same CATH topology
4Y52L 2YU9L 1TWAL 2E2HL 3GTJL 3GTOL 4AYBP 3HOYL 4A3LL 3GTGL 2PMZP 3GTKL 5IYBL 2R7ZL 3PO2L 3S1NL 1TWHL 3HOUL 3S1RL 2JA8L 2B63L 3RZDL 4A3GL 4BY1L 1WCML 3S1ML 1K83L 2WAQP 2E2JL 5IYDL 4QIWP 4C3IL 4BBRL 2JA5L 4A93L 3GTQL 4BBSL 2NVTL 2Y0SP 4A3IL 3HOZL 3S2DL 4A3JL 5M5XL 5IYCL 5FLML 2JA6L 4BXXL 5C4JL 3S16L 3GTML 3S17L 3S14L 2R93L 1TWCL 4BY7L 3RZOL 3S2HL 1Y1WL 5M5YL 1I6HL 5C44L 3PO3L 4C2M1 3H3VM 4A3DL 2WB1P 4A3EL 3S1QL 1SFOL 5FJ8L 3M4OL 1I50L 4X6AL 3I4NL 4A3FL 3HOXL 4C3JL 1TWGL 4C3HL 3FKIL 3S15L 3GTPL 2JA7L 2NVQL 3M3YL 5M3ML 1R9TL 3K7AL 5M5WL 1Y1VL 4A3CL 3HOWL 2VUML 3GTLL 5M3FL 3HKZP 4A3KL 5C3EL 2R92L 5C4XL 4Y7NL 4A3BL 3CQZL 4A3ML 2E2IL 3HOVL 3I4ML 2NVYL 3H0GL 5IP9L 5IP7L 2NVXL 1I3QL 1TWFL
chains in the Genus database with same CATH homology


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