4A3EL

Rna polymerase ii initial transcribing complex with a 5nt dna-rna hybrid and soaked with ampcpp
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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molecule tags Transcription
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
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 4a3eL00
2NVXL 5FLML 5M5WL 3S1RL 2JA8L 3CQZL 1I6HL 1TWFL 3GTPL 4BY1L 2R93L 1Y1WL 4A3ML 2PMZP 3HOXL 4A3KL 5IYBL 3HKZP 2R7ZL 3GTKL 5M5XL 2Y0SP 3GTLL 4A3IL 3HOUL 4Y7NL 2VUML 2E2IL 5C4XL 5FJ8L 1I3QL 3GTOL 4A3DL 3GTJL 2NVTL 2NVYL 2YU9L 4A3JL 4A3CL 2WB1P 3H0GL 1TWAL 4C3HL 3S2HL 3GTGL 5M3FL 2E2HL 5M5YL 2WAQP 4A3EL 1TWGL 2B63L 5C44L 3GTML 1WCML 5M3ML 3HOZL 3HOYL 1K83L 3HOVL 4X6AL 1TWHL 4A3LL 3PO3L 3PO2L 4C2M1 4A3GL 3S1ML 5IYCL 3S1NL 3S16L 3RZDL 4BBSL 4A3FL 2JA5L 5C4JL 3K7AL 3M3YL 4Y52L 4BY7L 4BBRL 5C3EL 3GTQL 1TWCL 3S15L 5IP9L 2JA6L 2R92L 3HOWL 4BXXL 3RZOL 3I4NL 2E2JL 3S2DL 3S17L 2NVQL 3S14L 4AYBP 5IP7L 4QIWP 1I50L 3S1QL 4C3JL 3FKIL 3M4OL 1R9TL 4A3BL 4C3IL 1Y1VL 1SFOL 4A93L 3H3VM 2JA7L 3I4ML 5IYDL
chains in the Genus database with same CATH superfamily
3HJWB 2NVXL 5FLML 5M5WL 1T9OA 4AI0A 1TWFL 2V3BB 1QCVA 2J9UB 3HAXC 4ME3A 3H97A 5M5XL 2Y0SP 3WWLA 3GTLL 1VZGA 1PFVA 2A6ED 3GTJL 2PVXA 2NVTL 1YV1A 3H99A 4A3CL 1BQ9A 2WB1P 3S2HL 3GTGL 4K9FA 5M3FL 3K35A 2ERSA 3RZ6A 1NXEA 4A3EL 2M6OA 1SMWA 2A69D 3FDJA 4E6YA 4ZN1B 4YWLA 1BRFA 1PFUA 3LWOB 3KYWA 2KN9A 1B2JA 4A3LL 2XJVA 4TPUA 4JAGA 3PO2L 3LWRB 6RXNA 1B13A 5K2ME 4ZN3B 2PYAA 1LKOA 3K7AL 4RXNA 4Y52L 1NXGA 3GTQL 1TWCL 4GS7D 3J7Y1 5MGNA 1VZIA 1IW7D 2CKAA 5IP9L 1CADA 2DSXA 2XJSA 2NVQL 1YK4A 4AYBP 2Z3QB 5MFZA 4QIWP 1I50L 4C3JL 2XJRA 3PL5A 1F4LA 4JAFA 4LHLA 3H9CA 1FHMA 2GMGA 1IU6A 2ERJA 1SFOL 1RB9A 4AHZA 1QQTA 2K2DA 4A93L 2PPTA 2XJPA 4AR6A 1B71A 5IYDL 5EINC 3KYUA 1S24A 1R0FA 2JI3A 2O5JD 3RZTA 8RXNA 3GTPL 3KYXA 2R93L 4A3ML 2CKCA 2PMZP 2M6PA 1SMMA 5JVH1 3GTOL 1YUZA 5MFPA 4AR5A 2NYDA 7RXNA 4A3JL 2A68D 1PZXA 4AR3A 4C3HL 3PIP1 2E2HL 5M5YL 2B63L 5C44L 2AUSB 1R0IA 3HOYL 5DM61 2RFKB 3PO3L 2XJQA 4C2M1 2KKDA 5GADc 1C09A 1LTLA 3S16L 1S2ZA 2PSMC 1B2OA 1RDVA 3M3YL 4BY7L 4B8CD 2RDVA 1IROA 3S15L 4AHWA 3MQKB 3HOWL 4G6BA 4U671 1YUXA 2L0ZA 3PIO1 1NNQA 1QYBA 3S14L 1R0JA 5RXNA 2H12A 3S1QL 3P8BA 3VPBE 1R9TL 1CAAA 4C3IL 5DM71 2A6HD 3A44A 3HJYB 1BE7A 2JA7L 3I4ML 2JI2A 2PVEA 1T9PA 3PKJA 3KYVA 3IU3I 1I6HL 4JAEA 1Y1WL 4AHXA 1WJVA 3HKZP 3LPEB 1ZRPA 5IY0A 3PWFA 3HOUL 3LWPB 2C6AA 5C4XL 1FHHA 3LWVB 2NVYL 2YU9L 3H0GL 3H9BA 1VZHA 2JI1A 5GAEc 2XJUA 2WAQP 2APOB 2CR8A 2V0EA 3LNLA 5M3ML 1PFWA 1LKPA 1K83L 3HOVL 5GAGc 4POFA 1TWHL 4UY81 3S1ML 2V0FA 4POGA 5IYCL 1P7PA 2EY4E 1SMUA 2JA5L 2MS3A 5C4JL 3LWQB 3JR7A 2LCQA 4BBRL 2AYJA 5EIOC 1IU5A 1T9QA 2JA6L 4V196 2R92L 4BXXL 2Z3RB 3S17L 2XJTA 3FKIL 2QL0A 3MPSA 1YK5A 2BE5D 4YWMA 4A3BL 1BFYA 4AR4A 3S1RL 2B5ID 2JA8L 3WWNB 3CQZL 4AI2A 3J7Z1 1ODHA 4BY1L 1PFYA 4LHNA 1H7VA 5GAHc 2VL6A 3P2AA 2HR5A 3HOXL 4A3KL 5AI2A 5IYBL 1RYQA 2R7ZL 3GTKL 3B0AB 1JYBA 4A3IL 4Y7NL 1OWCA 2VUML 2E2IL 5FJ8L 1I3QL 4A3DL 1OWBA 3NFPI 1TWAL 3ZG6A 5MLC3 1IRNA 1Z92B 4WFN1 2AQCA 1LKMA 1TWGL 4AI3A 3GTML 1WCML 4XGHA 1DX8A 3HOZL 1R0GA 3RYGA 3KYYA 1RWDA 4X6AL 5AN9H 4A3GL 5MF6A 4XXBB 3S1NL 2HVYC 1S30A 3RZDL 4BBSL 4A3FL 3PKIA 4TVMA 1R0HA 4AI1A 1RDGA 5C3EL 5JVG1 4JADA 2ZIXA 3B08B 3RZOL 3PZAA 3I4NL 2E2JL 3S2DL 4AHYA 1BQ8A 3QVDA 2C6BA 5IP7L 1E8JA 3SS2A 5H1Sc 3QQCE 3M4OL 3MSUA 2M4VA 1Y1VL 2M4YA 1VCXA 5AI3A 3H3VM 1RYTA 1DVBA
chains in the Genus database with same CATH topology
2NVXL 5FLML 5M5WL 3S1RL 2JA8L 3CQZL 1I6HL 1TWFL 3GTPL 4BY1L 2R93L 1Y1WL 4A3ML 2PMZP 3HOXL 4A3KL 5IYBL 3HKZP 2R7ZL 3GTKL 5M5XL 2Y0SP 3GTLL 4A3IL 3HOUL 4Y7NL 2VUML 2E2IL 5C4XL 5FJ8L 1I3QL 3GTOL 4A3DL 3GTJL 2NVTL 2NVYL 2YU9L 4A3JL 4A3CL 2WB1P 3H0GL 1TWAL 4C3HL 3S2HL 3GTGL 5M3FL 2E2HL 5M5YL 2WAQP 4A3EL 1TWGL 2B63L 5C44L 3GTML 1WCML 5M3ML 3HOZL 3HOYL 1K83L 3HOVL 4X6AL 1TWHL 4A3LL 3PO3L 3PO2L 4C2M1 4A3GL 3S1ML 5IYCL 3S1NL 3S16L 3RZDL 4BBSL 4A3FL 2JA5L 5C4JL 3K7AL 3M3YL 4Y52L 4BY7L 4BBRL 5C3EL 3GTQL 1TWCL 3S15L 5IP9L 2JA6L 2R92L 3HOWL 4BXXL 3RZOL 3I4NL 2E2JL 3S2DL 3S17L 2NVQL 3S14L 4AYBP 5IP7L 4QIWP 1I50L 3S1QL 4C3JL 3FKIL 3M4OL 1R9TL 4A3BL 4C3IL 1Y1VL 1SFOL 4A93L 3H3VM 2JA7L 3I4ML 5IYDL
chains in the Genus database with same CATH homology


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