4A3ML

Rna polymerase ii initial transcribing complex with a 4nt 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 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 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 4a3mL00
2JA7L 3HKZP 3S14L 2NVXL 4C2M1 4Y7NL 2JA5L 3S1QL 1Y1VL 2R7ZL 3M4OL 1K83L 4BY7L 2Y0SP 4A3JL 3FKIL 3HOXL 1Y1WL 3K7AL 2R92L 2JA6L 2B63L 5M5XL 4A93L 4C3HL 4A3CL 3S1RL 5IYCL 4A3DL 4QIWP 2YU9L 4C3IL 4BBSL 4A3FL 3PO3L 5M5WL 3RZDL 2E2IL 4BY1L 2NVYL 3S1ML 1I50L 2JA8L 3GTML 5C4XL 2PMZP 3HOUL 3HOZL 4Y52L 4A3EL 3H0GL 1I6HL 3I4NL 1TWHL 3GTGL 3M3YL 1WCML 2NVQL 4BBRL 4X6AL 2NVTL 3RZOL 2R93L 5IP9L 2WB1P 5FJ8L 3GTKL 3GTJL 5C44L 3HOYL 3I4ML 1TWCL 1TWFL 5M5YL 4A3GL 4A3BL 3S1NL 5M3ML 5M3FL 3GTPL 3H3VM 5C4JL 3GTLL 3PO2L 4A3IL 2E2HL 4A3ML 5IP7L 3S17L 4A3KL 1SFOL 3GTQL 3HOWL 4AYBP 1I3QL 4A3LL 4C3JL 5IYDL 1R9TL 5IYBL 3S16L 1TWAL 3HOVL 2E2JL 4BXXL 1TWGL 5C3EL 2VUML 5FLML 3CQZL 3S2HL 3S15L 3S2DL 3GTOL 2WAQP
chains in the Genus database with same CATH superfamily
2XJUA 1RYQA 4C2M1 4TVMA 1Y1VL 4YWLA 5MF6A 2Z3RB 4AR6A 4C3HL 2CKAA 3FDJA 3K35A 1PFVA 2YU9L 4G6BA 3PO3L 1YV1A 4BY1L 2HR5A 2NVYL 3ZG6A 1I50L 1SMWA 1PFUA 1BQ9A 5EINC 1JYBA 1RDGA 1WJVA 1LKPA 4POGA 4AI3A 1TWHL 3GTGL 3M3YL 3B08B 2NVQL 4BBRL 1SMMA 2H12A 2R93L 1VZIA 2XJSA 1IU5A 3I4ML 1TWCL 2JI3A 1TWFL 2V3BB 3J7Z1 5DM61 2PVXA 1C09A 3S1NL 1T9OA 3GTPL 1BQ8A 1LKMA 4YWMA 1Z92B 3PO2L 1BFYA 1B2OA 4A3IL 4AI1A 2XJTA 3H99A 4U671 2E2HL 1PFWA 4A3ML 1SFOL 1YUXA 2RDVA 3HAXC 4C3JL 4AI2A 4POFA 2JI2A 1DVBA 3JR7A 1TWAL 4BXXL 1P7PA 5GAHc 2O5JD 1YK4A 3S15L 3S2DL 3PKJA 3P2AA 4JAEA 1PFYA 4ME3A 1YK5A 3S14L 3H97A 1ODHA 5MLC3 3H9BA 3S1QL 2AYJA 2RFKB 1B71A 1R0FA 3PZAA 8RXNA 2CR8A 3FKIL 4JAFA 4AHWA 3LWRB 3HOXL 2A6HD 2R92L 1LKOA 2JA6L 1FHMA 2M4VA 2AQCA 3PL5A 4WFN1 3S1RL 1IRNA 1BE7A 3KYWA 5AN9H 1B2JA 4C3IL 1E8JA 4AHZA 1RWDA 3LWOB 3GTML 5C4XL 3I4NL 1F4LA 3WWLA 3LWPB 3RZTA 1WCML 1NXGA 1IW7D 1CADA 2C6AA 5FJ8L 3GTKL 3PKIA 2AUSB 1R0GA 1SMUA 4A3BL 3LNLA 5DM71 2V0EA 2A6ED 5AI3A 4ZN3B 3H3VM 5C4JL 2LCQA 6RXNA 5AI2A 1RB9A 5IP7L 1PZXA 5MGNA 2KKDA 2PYAA 3GTQL 3HOWL 1I3QL 1QYBA 4JAGA 2XJPA 3S16L 5MFZA 1S2ZA 1LTLA 2JI1A 4UY81 2ZIXA 2ERSA 3MPSA 2NYDA 5C3EL 4GS7D 4XGHA 2VUML 5GAGc 5RXNA 5FLML 3S2HL 4AR3A 3KYVA 1S24A 3GTOL 2WAQP 3HKZP 1R0HA 3KYXA 2NVXL 2JA5L 4E6YA 2VL6A 3M4OL 1K83L 4BY7L 2Y0SP 4A3JL 4JADA 2GMGA 1Y1WL 3K7AL 3QQCE 1ZRPA 1DX8A 5M5XL 4A3CL 1VCXA 4K9FA 5IYCL 4A3DL 4QIWP 2Z3QB 3S1ML 5JVH1 2JA8L 3HOZL 4Y52L 1QCVA 3SS2A 4A3EL 3H0GL 1I6HL 1VZGA 3MSUA 5IY0A 5JVG1 3PWFA 4ZN1B 3VPBE 2HVYC 2EY4E 3LWVB 2K2DA 4X6AL 2NVTL 3RZOL 5IP9L 2WB1P 2CKCA 3GTJL 5C44L 2V0FA 1FHHA 1OWCA 5M3ML 7RXNA 3WWNB 5M3FL 2M4YA 3MQKB 2B5ID 1YUZA 1OWBA 1RYTA 1RDVA 3S17L 2PSMC 4RXNA 4V196 1S30A 4AHYA 4A3LL 5GADc 5IYDL 3QVDA 1VZHA 1R0JA 1B13A 5IYBL 1NNQA 5GAEc 2E2JL 5H1Sc 1TWGL 2ERJA 3J7Y1 4AR5A 5EIOC 2A68D 2JA7L 3PIO1 5K2ME 4Y7NL 2R7ZL 1CAAA 4AI0A 2QL0A 1IROA 2PPTA 2MS3A 1T9QA 3P8BA 2B63L 2KN9A 4A93L 1QQTA 4XXBB 4BBSL 4A3FL 4AHXA 3HJWB 3LPEB 4B8CD 5M5WL 3RZDL 2E2IL 3KYUA 3LWQB 1IU6A 2PMZP 3HOUL 2APOB 3HJYB 1BRFA 4TPUA 3NFPI 3RYGA 2L0ZA 5MFPA 2DSXA 2XJQA 3HOYL 3B0AB 1H7VA 5M5YL 4A3GL 2XJRA 4AR4A 4LHNA 2BE5D 3GTLL 4LHLA 2PVEA 1NXEA 4A3KL 2J9UB 2C6BA 3IU3I 4AYBP 1R9TL 3KYYA 2M6PA 2A69D 3RZ6A 1R0IA 2M6OA 3HOVL 3CQZL 3A44A 3H9CA 1T9PA 3PIP1 2XJVA
chains in the Genus database with same CATH topology
2JA7L 3HKZP 3S14L 2NVXL 4C2M1 4Y7NL 2JA5L 3S1QL 1Y1VL 2R7ZL 3M4OL 1K83L 4BY7L 2Y0SP 4A3JL 3FKIL 3HOXL 1Y1WL 3K7AL 2R92L 2JA6L 2B63L 5M5XL 4A93L 4C3HL 4A3CL 3S1RL 5IYCL 4A3DL 4QIWP 2YU9L 4C3IL 4BBSL 4A3FL 3PO3L 5M5WL 3RZDL 2E2IL 4BY1L 2NVYL 3S1ML 1I50L 2JA8L 3GTML 5C4XL 2PMZP 3HOUL 3HOZL 4Y52L 4A3EL 3H0GL 1I6HL 3I4NL 1TWHL 3GTGL 3M3YL 1WCML 2NVQL 4BBRL 4X6AL 2NVTL 3RZOL 2R93L 5IP9L 2WB1P 5FJ8L 3GTKL 3GTJL 5C44L 3HOYL 3I4ML 1TWCL 1TWFL 5M5YL 4A3GL 4A3BL 3S1NL 5M3ML 5M3FL 3GTPL 3H3VM 5C4JL 3GTLL 3PO2L 4A3IL 2E2HL 4A3ML 5IP7L 3S17L 4A3KL 1SFOL 3GTQL 3HOWL 4AYBP 1I3QL 4A3LL 4C3JL 5IYDL 1R9TL 5IYBL 3S16L 1TWAL 3HOVL 2E2JL 4BXXL 1TWGL 5C3EL 2VUML 5FLML 3CQZL 3S2HL 3S15L 3S2DL 3GTOL 2WAQP
chains in the Genus database with same CATH homology


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