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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molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
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
2JA8L 2NVQL 1I3QL 2YU9L 5M3ML 3H0GL 2NVTL 4C2M1 1TWAL 3HOXL 4AYBP 2VUML 1K83L 4C3JL 1I6HL 4BY1L 3CQZL 5C4XL 2WB1P 4X6AL 5M5XL 3HOUL 3I4ML 3S1RL 4A3FL 3GTPL 5M5WL 5IYCL 3GTLL 3GTGL 4BBSL 4C3IL 4QIWP 4A3DL 3FKIL 2JA5L 2PMZP 4BY7L 3GTJL 5FLML 1SFOL 4C3HL 3S1ML 3HOVL 1R9TL 4A93L 2R7ZL 3RZOL 3S16L 3GTOL 3H3VM 5M3FL 5IYDL 3S17L 4A3CL 3S1NL 2R93L 5IP9L 3HOWL 4Y7NL 1WCML 5IP7L 4BXXL 2JA7L 1Y1VL 1TWCL 3HOZL 5IYBL 3S2HL 4A3EL 3HOYL 3S14L 5FJ8L 4A3GL 4A3ML 1I50L 5C3EL 3I4NL 2B63L 2Y0SP 4BBRL 1TWHL 2E2HL 5M5YL 3GTQL 2E2IL 3S1QL 4A3KL 2JA6L 3M4OL 3RZDL 3S2DL 3K7AL 3GTKL 1TWGL 1TWFL 2NVYL 1Y1WL 3PO2L 5C4JL 5C44L 4A3IL 2WAQP 4Y52L 2NVXL 3S15L 2E2JL 2R92L 4A3JL 3PO3L 3GTML 4A3BL 3M3YL 4A3LL 3HKZP
chains in the Genus database with same CATH superfamily
1SMWA 1NXGA 1I3QL 5M3ML 3H0GL 3NFPI 1YUZA 2XJUA 2K2DA 3LNLA 1VCXA 3CQZL 2WB1P 3I4ML 2APOB 3GTLL 1SMUA 3ZG6A 4QIWP 1FHMA 4AR5A 3GTJL 5FLML 1NXEA 4AI2A 1C09A 5EIOC 3S1ML 1OWBA 4TVMA 3JR7A 3PKJA 1RDVA 6RXNA 3H3VM 1RYQA 4AI3A 2A6HD 2AUSB 1JYBA 4JAGA 3HOWL 2ERJA 5JVH1 2JA7L 1VZHA 1E8JA 1TWCL 5MLC3 3LWQB 5IYBL 2LCQA 1B2JA 4YWMA 2A6ED 8RXNA 4A3ML 4POFA 1PFVA 1NNQA 3H99A 2Y0SP 2B63L 1TWHL 3KYVA 2E2HL 1RWDA 3MPSA 4WFN1 5DM71 3RZDL 2PPTA 1IU6A 1DX8A 7RXNA 1S30A 1TWGL 4AR6A 1T9OA 3IU3I 3LWRB 2V0EA 1BQ9A 1Y1WL 3PO2L 3KYWA 4K9FA 5GAGc 4Y52L 4JAEA 4U671 4A3JL 4A3BL 4A3LL 3PKIA 2NVQL 5RXNA 1TWAL 3HOXL 2A69D 1B2OA 2V3BB 1I6HL 1IW7D 3SS2A 5C4XL 4X6AL 5M5XL 2XJVA 3K35A 5MFPA 1B13A 1VZIA 5M5WL 5IYCL 1YUXA 3GTGL 4AR3A 4B8CD 1DVBA 2JA5L 2PMZP 1LKOA 4GS7D 4BY7L 1R0IA 3PIO1 1SFOL 2DSXA 2PYAA 2V0FA 2R7ZL 3S16L 1B71A 3J7Y1 3KYXA 5IYDL 4UY81 2R93L 1ODHA 2XJSA 5EINC 5IY0A 3P8BA 5GADc 5IP7L 2KN9A 3S2HL 4A3GL 4AHYA 1Z92B 1RYTA 5M5YL 4JADA 4A3KL 3B08B 4ZN1B 2JA6L 1PZXA 1TWFL 2KKDA 2C6AA 4V196 1PFYA 5C44L 2E2JL 2ZIXA 3GTML 2J9UB 1QCVA 3QQCE 4AHXA 1SMMA 3LWPB 4RXNA 3QVDA 2JI3A 2CR8A 4AYBP 3LWOB 1IROA 1K83L 4C3JL 4BY1L 3HJYB 1LKMA 5H1Sc 3S1RL 4A3FL 1QYBA 2RFKB 4C3IL 2XJQA 4LHLA 4A3DL 3FKIL 2PVEA 2A68D 1LKPA 5AI3A 1LTLA 3HOVL 3H9BA 1S2ZA 2HR5A 1R9TL 3RZOL 2MS3A 3GTOL 1R0HA 5M3FL 2Z3QB 5IP9L 2AYJA 4Y7NL 2PSMC 2PVXA 1Y1VL 1RB9A 5MF6A 4E6YA 3HAXC 2B5ID 4A3EL 1H7VA 4YWLA 5DM61 3HOYL 3S14L 3WWNB 1YK5A 4TPUA 4AHZA 3HJWB 3H97A 3KYYA 1BQ8A 4BBRL 2XJTA 2QL0A 3GTQL 1CAAA 2E2IL 3S1QL 1PFUA 1ZRPA 2O5JD 3S2DL 2JI2A 3GTKL 4POGA 2Z3RB 1YV1A 4AI1A 3P2AA 5C4JL 2GMGA 3PL5A 2C6BA 1QQTA 3WWLA 2WAQP 2NVXL 1P7PA 1IRNA 3PO3L 2ERSA 2AQCA 3PZAA 3HKZP 1IU5A 4XXBB 4AI0A 2JA8L 2YU9L 5GAHc 2NVTL 3B0AB 4C2M1 3H9CA 2NYDA 3MSUA 2VUML 1PFWA 2M6OA 3KYUA 4LHNA 3HOUL 4AHWA 1R0FA 3GTPL 3A44A 3RZ6A 4BBSL 1WJVA 4AR4A 2BE5D 4G6BA 5AN9H 1FHHA 3PWFA 1YK4A 4C3HL 2L0ZA 2JI1A 1VZGA 3LPEB 3J7Z1 4A93L 5K2ME 2VL6A 3LWVB 5MFZA 5AI2A 1T9PA 3PIP1 1RDGA 1F4LA 2M4VA 3S17L 1BE7A 4A3CL 3S1NL 2CKCA 4ME3A 2H12A 1R0GA 1R0JA 5JVG1 1OWCA 1WCML 4BXXL 5GAEc 2XJRA 1S24A 3HOZL 1BFYA 2XJPA 1BRFA 5FJ8L 2M6PA 3MQKB 1I50L 5C3EL 3I4NL 4XGHA 5MGNA 2EY4E 4ZN3B 3M4OL 3FDJA 3K7AL 4JAFA 3RYGA 2RDVA 3RZTA 2NVYL 1CADA 2M4YA 4A3IL 3S15L 3VPBE 2CKAA 2R92L 1T9QA 2HVYC 3M3YL
chains in the Genus database with same CATH topology
2JA8L 2NVQL 1I3QL 2YU9L 5M3ML 3H0GL 2NVTL 4C2M1 1TWAL 3HOXL 4AYBP 2VUML 1K83L 4C3JL 1I6HL 4BY1L 3CQZL 5C4XL 2WB1P 4X6AL 5M5XL 3HOUL 3I4ML 3S1RL 4A3FL 3GTPL 5M5WL 5IYCL 3GTLL 3GTGL 4BBSL 4C3IL 4QIWP 4A3DL 3FKIL 2JA5L 2PMZP 4BY7L 3GTJL 5FLML 1SFOL 4C3HL 3S1ML 3HOVL 1R9TL 4A93L 2R7ZL 3RZOL 3S16L 3GTOL 3H3VM 5M3FL 5IYDL 3S17L 4A3CL 3S1NL 2R93L 5IP9L 3HOWL 4Y7NL 1WCML 5IP7L 4BXXL 2JA7L 1Y1VL 1TWCL 3HOZL 5IYBL 3S2HL 4A3EL 3HOYL 3S14L 5FJ8L 4A3GL 4A3ML 1I50L 5C3EL 3I4NL 2B63L 2Y0SP 4BBRL 1TWHL 2E2HL 5M5YL 3GTQL 2E2IL 3S1QL 4A3KL 2JA6L 3M4OL 3RZDL 3S2DL 3K7AL 3GTKL 1TWGL 1TWFL 2NVYL 1Y1WL 3PO2L 5C4JL 5C44L 4A3IL 2WAQP 4Y52L 2NVXL 3S15L 2E2JL 2R92L 4A3JL 3PO3L 3GTML 4A3BL 3M3YL 4A3LL 3HKZP
chains in the Genus database with same CATH homology


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