4A3FL

Rna polymerase ii initial transcribing complex with a 6nt dna-rna hybrid and soaked with ampcpp
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 4a3fL00
3M4OL 5M3ML 4A93L 2VUML 5C3EL 4Y52L 3I4NL 5C4XL 5FJ8L 3H3VM 4A3GL 4A3JL 3S17L 3S15L 5M5XL 2JA6L 2NVTL 2JA8L 2E2IL 4AYBP 4BXXL 1TWFL 3GTPL 4C2M1 3GTQL 3PO3L 5M5WL 5C44L 3HOUL 2R92L 4A3CL 3M3YL 5IYCL 3HOZL 2R7ZL 2NVYL 1TWHL 4A3IL 4C3JL 3HOWL 2YU9L 1TWGL 4A3BL 3K7AL 3RZDL 1TWCL 1I50L 3S1RL 3HOYL 3PO2L 3S2HL 2JA5L 3S14L 3HKZP 2WB1P 5IYBL 4A3KL 3I4ML 4QIWP 3GTLL 4A3DL 3H0GL 5IP9L 3S16L 2Y0SP 4C3HL 3GTKL 5IP7L 3S1NL 4A3LL 4BY7L 3S1ML 1Y1WL 5C4JL 2JA7L 1WCML 5FLML 3GTJL 1K83L 4A3EL 4BBRL 3GTOL 3GTML 1I6HL 1R9TL 1I3QL 3S2DL 5IYDL 4A3FL 2PMZP 3HOVL 4A3ML 5M3FL 4BY1L 4C3IL 3GTGL 3FKIL 2B63L 1TWAL 4Y7NL 3CQZL 1SFOL 3HOXL 2NVQL 2E2HL 2R93L 5M5YL 2E2JL 3S1QL 4X6AL 1Y1VL 2NVXL 2WAQP 3RZOL 4BBSL
chains in the Genus database with same CATH superfamily
3M4OL 2XJRA 4POFA 3LWQB 1LKOA 1PFVA 3LNLA 4Y52L 1JYBA 5C4XL 1RYTA 1YK5A 2KKDA 1BRFA 2RDVA 1VZGA 2JA8L 4AHZA 3GTPL 1NNQA 3GTQL 1YV1A 4AHWA 2XJPA 1RWDA 2A6HD 3M3YL 5JVH1 2NVYL 5AI3A 2CKCA 2JI3A 3K7AL 5GAHc 1DVBA 3S1RL 3HOYL 2JA5L 2WB1P 1S2ZA 4A3DL 3H0GL 5IP9L 1BQ8A 2Y0SP 1RB9A 1PFWA 3H97A 1R0HA 3NFPI 1IU5A 3ZG6A 2PSMC 2KN9A 3P8BA 4UY81 3MSUA 4AHYA 2AUSB 1VZHA 1B2JA 1K83L 2PPTA 1QCVA 1I6HL 3KYUA 3PKIA 1B71A 4B8CD 4JAGA 1S30A 2XJUA 2ERJA 4C3IL 4AHXA 4Y7NL 2C6AA 1SFOL 3KYYA 1RYQA 1R0JA 8RXNA 4X6AL 1FHMA 2APOB 3KYXA 4JAEA 5MF6A 3RZOL 1FHHA 2CR8A 2PYAA 3LWPB 3PIP1 2V0EA 1BQ9A 1QQTA 3H9CA 1QYBA 5AI2A 5EINC 4V196 5FJ8L 3P2AA 2ERSA 5M5XL 2JA6L 3RYGA 2NVTL 4AYBP 4XGHA 4C2M1 1SMUA 3QQCE 5M5WL 3HOUL 3IU3I 2R92L 5IYCL 2R7ZL 1PFUA 3HOWL 1TWGL 2XJQA 3RZDL 1NXGA 5K2ME 2M4YA 3LWVB 3S14L 4AI1A 4A3KL 5IYBL 3GTLL 3K35A 3RZ6A 1ZRPA 4ME3A 1NXEA 3HJWB 1PZXA 1BE7A 2ZIXA 4BY7L 1YUXA 3J7Y1 2HVYC 3S1ML 1P7PA 4YWMA 4AR6A 5GAGc 2M6OA 1WCML 2J9UB 4AI3A 4A3EL 1R0GA 4BBRL 1H7VA 5AN9H 5IYDL 1DX8A 3HOVL 4A3ML 1T9PA 4BY1L 3GTGL 3MQKB 4AR3A 4JADA 1TWAL 1IW7D 4U671 2XJSA 2NVQL 5RXNA 5GADc 2E2HL 5M5YL 1WJVA 2M4VA 1E8JA 4BBSL 1BFYA 2L0ZA 4A93L 3PZAA 4LHLA 1VZIA 2VUML 5C3EL 2JI2A 3KYWA 3PKJA 1IROA 4ZN3B 2AQCA 4A3JL 3S17L 3S15L 5MGNA 5IY0A 5DM61 2E2IL 4BXXL 1TWFL 3H9BA 3PO3L 5MFZA 2JI1A 2C6BA 5C44L 3LWOB 2NYDA 3A44A 3HOZL 2XJTA 4A3IL 4C3JL 2YU9L 2RFKB 4AR5A 2HR5A 3WWNB 3PO2L 4RXNA 3HKZP 2LCQA 3I4ML 1B13A 2A68D 7RXNA 4ZN1B 4C3HL 4E6YA 3GTKL 5IP7L 3KYVA 1SMWA 3WWLA 4A3LL 4XXBB 4AI0A 1Y1WL 5C4JL 2M6PA 5DM71 2CKAA 3S2DL 1R9TL 4AR4A 1PFYA 1VCXA 2PVXA 5M3FL 1Z92B 2GMGA 3FKIL 1S24A 1OWCA 3MPSA 3B0AB 2R93L 2E2JL 3S1QL 3RZTA 2NVXL 2WAQP 3B08B 5MFPA 3H99A 4WFN1 5M3ML 4AI2A 3PWFA 2AYJA 3I4NL 1LKPA 1R0FA 3HJYB 1CADA 3H3VM 4GS7D 4A3GL 4JAFA 1CAAA 5GAEc 1IU6A 5EIOC 2O5JD 2B5ID 3SS2A 3VPBE 2H12A 2QL0A 5JVG1 2V0FA 3FDJA 4A3CL 1LKMA 2EY4E 1C09A 1ODHA 2A6ED 1TWHL 5H1Sc 4A3BL 2DSXA 1B2OA 1TWCL 1I50L 1RDVA 1LTLA 3S2HL 4YWLA 4QIWP 2Z3RB 2VL6A 3LWRB 5MLC3 1YUZA 3S16L 1SMMA 1T9OA 6RXNA 2PVEA 3QVDA 4LHNA 3S1NL 2BE5D 4K9FA 2Z3QB 1F4LA 2JA7L 1YK4A 5FLML 3GTJL 2K2DA 3J7Z1 4G6BA 3GTOL 2V3BB 3GTML 4POGA 1I3QL 1R0IA 4A3FL 2PMZP 3PIO1 3HAXC 1IRNA 4TVMA 3JR7A 1RDGA 2XJVA 2B63L 3CQZL 3HOXL 4TPUA 2MS3A 3LPEB 1Y1VL 1T9QA 1OWBA 3PL5A 2A69D
chains in the Genus database with same CATH topology
3M4OL 5M3ML 4A93L 2VUML 5C3EL 4Y52L 3I4NL 5C4XL 5FJ8L 3H3VM 4A3GL 4A3JL 3S17L 3S15L 5M5XL 2JA6L 2NVTL 2JA8L 2E2IL 4AYBP 4BXXL 1TWFL 3GTPL 4C2M1 3GTQL 3PO3L 5M5WL 5C44L 3HOUL 2R92L 4A3CL 3M3YL 5IYCL 3HOZL 2R7ZL 2NVYL 1TWHL 4A3IL 4C3JL 3HOWL 2YU9L 1TWGL 4A3BL 3K7AL 3RZDL 1TWCL 1I50L 3S1RL 3HOYL 3PO2L 3S2HL 2JA5L 3S14L 3HKZP 2WB1P 5IYBL 4A3KL 3I4ML 4QIWP 3GTLL 4A3DL 3H0GL 5IP9L 3S16L 2Y0SP 4C3HL 3GTKL 5IP7L 3S1NL 4A3LL 4BY7L 3S1ML 1Y1WL 5C4JL 2JA7L 1WCML 5FLML 3GTJL 1K83L 4A3EL 4BBRL 3GTOL 3GTML 1I6HL 1R9TL 1I3QL 3S2DL 5IYDL 4A3FL 2PMZP 3HOVL 4A3ML 5M3FL 4BY1L 4C3IL 3GTGL 3FKIL 2B63L 1TWAL 4Y7NL 3CQZL 1SFOL 3HOXL 2NVQL 2E2HL 2R93L 5M5YL 2E2JL 3S1QL 4X6AL 1Y1VL 2NVXL 2WAQP 3RZOL 4BBSL
chains in the Genus database with same CATH homology


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