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


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