4A3DL

Rna polymerase ii initial transcribing complex with a 6nt dna-rna hybrid
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 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 2
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 4a3dL00
3M3YL 4A3CL 3GTPL 3GTQL 4C3JL 5IP7L 4BXXL 4BBSL 4QIWP 2JA6L 3I4NL 4A93L 5M5XL 1TWHL 3S1NL 5FLML 3FKIL 2WAQP 5M3FL 2R7ZL 3M4OL 4Y52L 1TWGL 3HOUL 1TWFL 3HOVL 1I3QL 4C2M1 2JA5L 4C3IL 3GTLL 1I6HL 3S17L 4A3JL 3HOYL 4A3GL 5C3EL 1WCML 4A3LL 1R9TL 2E2HL 4A3BL 3S15L 5IYBL 5M5YL 3GTOL 5C4XL 2R92L 3S2DL 3HOWL 1I50L 3RZOL 5FJ8L 3GTGL 3S1QL 5IYDL 1Y1VL 3PO3L 3CQZL 1SFOL 3RZDL 1Y1WL 2PMZP 5M3ML 2Y0SP 3S14L 2WB1P 4A3DL 1TWAL 3GTJL 4A3KL 4AYBP 2JA7L 2NVXL 3HOXL 3H3VM 4X6AL 4C3HL 4Y7NL 3GTML 4A3FL 2NVYL 2VUML 4BBRL 1TWCL 4A3IL 4BY1L 2JA8L 3GTKL 5M5WL 3S2HL 1K83L 2R93L 4A3ML 4BY7L 5IP9L 2E2IL 2YU9L 3H0GL 3HKZP 2E2JL 3S1ML 3K7AL 4A3EL 3I4ML 5IYCL 5C44L 2NVTL 2NVQL 3PO2L 5C4JL 2B63L 3HOZL 3S16L 3S1RL
chains in the Genus database with same CATH superfamily
3M3YL 2A6HD 3H9CA 2CKAA 1R0JA 1SMMA 3I4NL 4WFN1 1VZGA 2PVEA 3LWPB 2RFKB 3MQKB 1B13A 5M3FL 2R7ZL 1TWGL 5GAEc 1LKOA 3PIO1 2GMGA 4C3IL 3LPEB 2C6AA 3PWFA 1I6HL 5K2ME 1RYTA 2L0ZA 5C3EL 2LCQA 4AR5A 2E2HL 4JAEA 1YV1A 3S15L 5M5YL 2AQCA 5C4XL 3KYXA 4AHWA 4XXBB 2B5ID 2XJRA 3S1QL 1BE7A 2Z3RB 1R0IA 1R0GA 2HVYC 4GS7D 3S14L 4A3KL 2JA7L 2A68D 8RXNA 1FHHA 4A3FL 1NXEA 2V3BB 4K9FA 4AHYA 5GAHc 1K83L 3P8BA 1S24A 4BY7L 2XJTA 5H1Sc 2PVXA 2E2JL 3A44A 3K7AL 2ERSA 4JADA 5RXNA 1FHMA 4AI2A 3MSUA 1CAAA 3WWLA 3HOZL 5DM61 3S1RL 1B2OA 3H99A 4C3JL 4BXXL 4LHNA 4QIWP 2M4VA 5M5XL 3ZG6A 1C09A 2ZIXA 1TWHL 3S1NL 2CR8A 1B71A 3KYYA 3HOUL 3S17L 1OWCA 4A3JL 4A3GL 2XJUA 2MS3A 3LWQB 2JI1A 1H7VA 2M6PA 5MFPA 3GTOL 4POFA 2R92L 3S2DL 4ZN1B 3HOWL 2PPTA 1I50L 5GADc 5FJ8L 3GTGL 2APOB 3H97A 1VZIA 2VL6A 3LWOB 3SS2A 1T9QA 1YK5A 7RXNA 4JAFA 2AUSB 5M3ML 1TWAL 4ZN3B 2CKCA 1YUZA 3JR7A 2NVXL 3PIP1 1QYBA 1RYQA 3QQCE 4AHZA 4POGA 4Y7NL 3GTML 2NVYL 1BQ8A 4A3IL 4BY1L 4AR6A 3GTKL 4AI3A 4B8CD 5M5WL 2R93L 1T9PA 2JI2A 3H0GL 3I4ML 5IYCL 2BE5D 4AI1A 4ME3A 2NVQL 3PO2L 3PKJA 2O5JD 2RDVA 1BFYA 4LHLA 3S16L 3GTPL 3GTQL 5IP7L 2C6BA 1QCVA 2NYDA 2AYJA 4JAGA 4BBSL 1DX8A 1PFUA 2PSMC 4A93L 5GAGc 1S30A 1S2ZA 5FLML 3FKIL 2WAQP 4TPUA 5IY0A 3M4OL 1TWFL 1Z92B 1P7PA 1I3QL 1RWDA 1SMUA 3HJWB 1E8JA 3RYGA 4C2M1 2JA5L 5AN9H 2H12A 1CADA 1OWBA 3P2AA 3J7Y1 4AI0A 4V196 1YUXA 4A3LL 1LKPA 2Z3QB 3J7Z1 2QL0A 1B2JA 1JYBA 2DSXA 1F4LA 4YWLA 1NXGA 2A69D 1YK4A 5JVH1 2KKDA 4UY81 5IYDL 1Y1VL 1SMWA 3CQZL 1SFOL 5MLC3 1Y1WL 2PMZP 2J9UB 4RXNA 2ERJA 2WB1P 3LNLA 3HOXL 4X6AL 1RB9A 3KYWA 3K35A 4C3HL 4XGHA 2KN9A 5MF6A 3KYVA 2VUML 2EY4E 4BBRL 1TWCL 2JA8L 5MGNA 1PZXA 3KYUA 3IU3I 4A3ML 2YU9L 4U671 1RDGA 4A3EL 3HAXC 1VZHA 3LWRB 1QQTA 5C44L 2NVTL 1IU5A 1BQ9A 1VCXA 2PYAA 5C4JL 4AR4A 2V0FA 5DM71 1R0FA 4A3CL 2JA6L 5AI3A 3FDJA 1DVBA 2XJPA 6RXNA 4Y52L 4G6BA 3RZTA 3HOVL 4E6YA 3GTLL 1IW7D 4TVMA 1LKMA 2V0EA 3HOYL 2A6ED 1IROA 1ZRPA 3WWNB 1IU6A 1WCML 1R9TL 4A3BL 1WJVA 1PFVA 5IYBL 5MFZA 3H9BA 3PL5A 4AR3A 2HR5A 1NNQA 2XJVA 2JI3A 5EINC 3RZOL 3B08B 3VPBE 2M4YA 2M6OA 2K2DA 3HJYB 3LWVB 3PO3L 3RZDL 1PFYA 2Y0SP 4A3DL 3GTJL 5EIOC 3NFPI 4AYBP 3H3VM 4AHXA 2XJQA 1R0HA 2XJSA 3PKIA 3RZ6A 1RDVA 1PFWA 3B0AB 3S2HL 1IRNA 3MPSA 5AI2A 5IP9L 2E2IL 3PZAA 3HKZP 3S1ML 1ODHA 5JVG1 1BRFA 3QVDA 2B63L 4YWMA 1T9OA 1LTLA
chains in the Genus database with same CATH topology
3M3YL 4A3CL 3GTPL 3GTQL 4C3JL 5IP7L 4BXXL 4BBSL 4QIWP 2JA6L 3I4NL 4A93L 5M5XL 1TWHL 3S1NL 5FLML 3FKIL 2WAQP 5M3FL 2R7ZL 3M4OL 4Y52L 1TWGL 3HOUL 1TWFL 3HOVL 1I3QL 4C2M1 2JA5L 4C3IL 3GTLL 1I6HL 3S17L 4A3JL 3HOYL 4A3GL 5C3EL 1WCML 4A3LL 1R9TL 2E2HL 4A3BL 3S15L 5IYBL 5M5YL 3GTOL 5C4XL 2R92L 3S2DL 3HOWL 1I50L 3RZOL 5FJ8L 3GTGL 3S1QL 5IYDL 1Y1VL 3PO3L 3CQZL 1SFOL 3RZDL 1Y1WL 2PMZP 5M3ML 2Y0SP 3S14L 2WB1P 4A3DL 1TWAL 3GTJL 4A3KL 4AYBP 2JA7L 2NVXL 3HOXL 3H3VM 4X6AL 4C3HL 4Y7NL 3GTML 4A3FL 2NVYL 2VUML 4BBRL 1TWCL 4A3IL 4BY1L 2JA8L 3GTKL 5M5WL 3S2HL 1K83L 2R93L 4A3ML 4BY7L 5IP9L 2E2IL 2YU9L 3H0GL 3HKZP 2E2JL 3S1ML 3K7AL 4A3EL 3I4ML 5IYCL 5C44L 2NVTL 2NVQL 3PO2L 5C4JL 2B63L 3HOZL 3S16L 3S1RL
chains in the Genus database with same CATH homology


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