2YU9L

Rna polymerase ii elongation complex in 150 mm mg+2 with utp
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 5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'
publication title Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis
pubmed doi rcsb
molecule tags Transcription,transferase/dna-rna hybrid
total genus 1
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2007-04-06

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 2yu9L00
5C44L 5FJ8L 1TWAL 5M3ML 4A3ML 3HOWL 5IP9L 3CQZL 4Y52L 1Y1WL 2NVTL 3M3YL 3RZDL 3I4NL 1K83L 4A3JL 4A93L 5M5WL 4BBRL 2R93L 3GTOL 3GTKL 3GTLL 2PMZP 4A3CL 2YU9L 5C3EL 4C3HL 2B63L 3S2DL 5C4JL 3HOVL 3S1ML 4A3EL 3S1NL 1I6HL 2JA7L 1WCML 2WB1P 4A3FL 4BY7L 3PO3L 1TWFL 3S16L 5M3FL 2NVXL 2R7ZL 5M5XL 2JA8L 3K7AL 4BBSL 3HOUL 2VUML 2WAQP 4A3DL 1TWHL 4A3KL 4A3IL 2E2HL 1Y1VL 4C3JL 5IYBL 3S15L 3GTGL 4Y7NL 2R92L 4BY1L 3H3VM 2Y0SP 2NVYL 4QIWP 1SFOL 3RZOL 4C2M1 2E2JL 3GTQL 3S2HL 3GTJL 3HKZP 3PO2L 3M4OL 1I50L 2JA5L 5IYDL 2E2IL 4A3LL 5FLML 3HOXL 2JA6L 3H0GL 3S1QL 5IYCL 2NVQL 3S17L 4X6AL 4A3GL 4AYBP 4A3BL 1R9TL 3S1RL 5IP7L 5M5YL 5C4XL 1I3QL 4BXXL 3HOYL 1TWGL 3HOZL 3S14L 3FKIL 3GTML 4C3IL 3I4ML 3GTPL 1TWCL
chains in the Genus database with same CATH superfamily
5C44L 5FJ8L 1TWAL 4GS7D 5M3ML 4A3ML 1BQ8A 3PIO1 3VPBE 2K2DA 5IP9L 1IW7D 5EINC 4Y52L 3FDJA 3B08B 4AI0A 2M6PA 5GAGc 3KYVA 5M5WL 2R93L 4TPUA 1R0GA 1LTLA 5GADc 1PZXA 1QCVA 5C3EL 4C3HL 1WJVA 4AI2A 4ZN1B 1R0IA 3MSUA 3HOVL 3S1NL 2AQCA 1I6HL 2JA7L 3HAXC 4A3FL 3PWFA 3PO3L 4LHNA 3S16L 5M3FL 2A6HD 5GAEc 3SS2A 1R0JA 5MLC3 2E2HL 4A3IL 2V0EA 2RDVA 3GTGL 7RXNA 3KYWA 4QIWP 3RZTA 3RZOL 3GTQL 3PO2L 3M4OL 1I50L 2AUSB 2PVXA 5IYDL 1H7VA 2M6OA 3S1QL 2NVQL 3S17L 4X6AL 1VZHA 4XGHA 4ZN3B 1LKOA 3LWOB 5M5YL 3WWLA 1I3QL 4BXXL 1TWGL 1BQ9A 3FKIL 4AHWA 1F4LA 1IU6A 1QYBA 4YWLA 2JI1A 3CQZL 2JI2A 4WFN1 1PFYA 3LPEB 1PFWA 2XJVA 4BBRL 5DM61 3GTOL 2JI3A 1B71A 1RB9A 2PMZP 5IY0A 2YU9L 1ZRPA 3MPSA 2A69D 8RXNA 2V0FA 1S30A 1T9OA 1YK4A 2NVXL 5M5XL 3K7AL 2O5JD 1DVBA 1RYTA 1TWHL 1YV1A 4G6BA 3P2AA 4YWMA 2QL0A 4C3JL 2A68D 2ERJA 1VCXA 4Y7NL 5MGNA 3H3VM 5JVH1 2GMGA 4AR4A 1SMWA 3HKZP 4POFA 3J7Z1 4AR3A 2E2IL 3IU3I 4A3LL 3HOXL 3KYXA 2BE5D 2PPTA 4AR6A 3H0GL 3LNLA 4TVMA 5IYCL 3J7Y1 4AYBP 1IRNA 2C6BA 5IP7L 1S2ZA 1YK5A 3B0AB 3NFPI 3GTML 4C3IL 2XJTA 5JVG1 5K2ME 1Z92B 2HR5A 1Y1WL 2NVTL 2C6AA 2XJPA 3M3YL 1T9QA 5DM71 4JADA 1T9PA 3I4NL 4A3JL 3HJWB 4A93L 2XJQA 4JAGA 4ME3A 3GTKL 1IROA 2PVEA 5MFPA 5AN9H 2NYDA 5GAHc 3LWQB 3QQCE 2B63L 2KN9A 4AR5A 4AHZA 3A44A 1PFUA 2PSMC 3QVDA 3S1ML 2XJSA 2DSXA 2CKAA 2A6ED 3PIP1 1WCML 3H99A 4POGA 1S24A 4JAEA 4AHYA 2R7ZL 2ERSA 5RXNA 2VL6A 5AI2A 4A3DL 1SMMA 4JAFA 2MS3A 1Y1VL 1OWBA 2R92L 2XJRA 2H12A 2NVYL 4AHXA 3P8BA 1YUXA 4C2M1 2E2JL 3S2HL 3GTJL 3LWRB 1R0HA 2JA5L 1CAAA 4LHLA 5FLML 1FHHA 1ODHA 1PFVA 4V196 2J9UB 1RYQA 1B2OA 4E6YA 4A3GL 2L0ZA 1JYBA 1R9TL 3HJYB 3K35A 5MFZA 5C4XL 3PKIA 3LWPB 3HOZL 3S14L 2CR8A 2Z3QB 1IU5A 1RWDA 2ZIXA 3H9BA 3HOWL 1CADA 2Z3RB 5AI3A 3RZDL 1SMUA 1K83L 2XJUA 1LKPA 3ZG6A 1P7PA 3GTLL 2LCQA 5EIOC 4A3CL 4UY81 3RYGA 1BRFA 3WWNB 3S2DL 1NNQA 3PL5A 5C4JL 1QQTA 3PKJA 4U671 4A3EL 1E8JA 2M4YA 3RZ6A 1OWCA 2WB1P 4RXNA 4BY7L 1FHMA 4B8CD 1TWFL 2M4VA 5MF6A 2AYJA 2APOB 2JA8L 4BBSL 3HOUL 2VUML 2HVYC 2WAQP 4A3KL 1NXEA 6RXNA 2CKCA 3KYYA 5IYBL 1RDVA 3S15L 1NXGA 3H97A 4BY1L 2Y0SP 1RDGA 1SFOL 1BFYA 3LWVB 2EY4E 1B2JA 3H9CA 3MQKB 1R0FA 4AI1A 2JA6L 4K9FA 1B13A 2RFKB 2PYAA 3JR7A 4XXBB 2V3BB 5H1Sc 1C09A 1LKMA 3KYUA 4A3BL 1DX8A 1BE7A 3S1RL 3PZAA 4AI3A 2KKDA 1VZGA 3HOYL 2B5ID 1VZIA 3I4ML 3GTPL 1TWCL 1YUZA
chains in the Genus database with same CATH topology
5C44L 5FJ8L 1TWAL 5M3ML 4A3ML 3HOWL 5IP9L 3CQZL 4Y52L 1Y1WL 2NVTL 3M3YL 3RZDL 3I4NL 1K83L 4A3JL 4A93L 5M5WL 4BBRL 2R93L 3GTOL 3GTKL 3GTLL 2PMZP 4A3CL 2YU9L 5C3EL 4C3HL 2B63L 3S2DL 5C4JL 3HOVL 3S1ML 4A3EL 3S1NL 1I6HL 2JA7L 1WCML 2WB1P 4A3FL 4BY7L 3PO3L 1TWFL 3S16L 5M3FL 2NVXL 2R7ZL 5M5XL 2JA8L 3K7AL 4BBSL 3HOUL 2VUML 2WAQP 4A3DL 1TWHL 4A3KL 4A3IL 2E2HL 1Y1VL 4C3JL 5IYBL 3S15L 3GTGL 4Y7NL 2R92L 4BY1L 3H3VM 2Y0SP 2NVYL 4QIWP 1SFOL 3RZOL 4C2M1 2E2JL 3GTQL 3S2HL 3GTJL 3HKZP 3PO2L 3M4OL 1I50L 2JA5L 5IYDL 2E2IL 4A3LL 5FLML 3HOXL 2JA6L 3H0GL 3S1QL 5IYCL 2NVQL 3S17L 4X6AL 4A3GL 4AYBP 4A3BL 1R9TL 3S1RL 5IP7L 5M5YL 5C4XL 1I3QL 4BXXL 3HOYL 1TWGL 3HOZL 3S14L 3FKIL 3GTML 4C3IL 3I4ML 3GTPL 1TWCL
chains in the Genus database with same CATH homology


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