4A3LL

Rna polymerase ii initial transcribing complex with a 7nt 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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publication title Structural basis of initial RNA polymerase II transcription.
pubmed doi rcsb
molecule keywords DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
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 4a3lL00
1I6HL 2NVXL 2JA8L 2YU9L 1I50L 4BY7L 3S1NL 4BY1L 2B63L 2R93L 5C4JL 4QIWP 3GTLL 2R92L 3GTML 4BXXL 4A3DL 1Y1WL 5IP7L 3HOYL 2JA7L 4A93L 1R9TL 3GTKL 1TWHL 4A3KL 4A3ML 2NVQL 3GTGL 3S15L 4A3GL 2VUML 2JA5L 5IYDL 4A3CL 5FLML 3S17L 1TWCL 5M3FL 4A3FL 1WCML 4A3EL 3GTPL 5C4XL 1Y1VL 3M4OL 3HOWL 2WB1P 3S2HL 4BBRL 5IP9L 4A3LL 4A3JL 5M5YL 4C3IL 4C3HL 3I4NL 3FKIL 5M3ML 4A3BL 3PO2L 3H3VM 2R7ZL 4A3IL 4Y52L 3K7AL 3GTJL 2JA6L 2E2JL 3PO3L 1SFOL 3H0GL 3S1QL 5C44L 5M5XL 3S16L 1TWFL 2E2IL 3S1ML 5IYBL 2Y0SP 1TWGL 3GTQL 2NVYL 3CQZL 2NVTL 3GTOL 2PMZP 2E2HL 3HOZL 2WAQP 3RZDL 3S1RL 3M3YL 3HKZP 5M5WL 1I3QL 3HOVL 5IYCL 3HOUL 5C3EL 4AYBP 5FJ8L 4BBSL 1TWAL 4X6AL 3S2DL 4C3JL 4Y7NL 3RZOL 4C2M1 3HOXL 1K83L 3S14L 3I4ML
chains in the Genus database with same CATH superfamily
3NFPI 1I6HL 2NVXL 2XJRA 4BY7L 3GTML 1IROA 1QQTA 4JAEA 3MPSA 3LNLA 2J9UB 2M4VA 1R9TL 4RXNA 5MGNA 4A3GL 4JADA 2ERJA 4XGHA 5JVH1 3S17L 3P8BA 1TWCL 4JAGA 5M3FL 1YUZA 2LCQA 4UY81 4LHNA 3HOWL 2WB1P 5EINC 2CR8A 5IP9L 3FDJA 5M5YL 3PKJA 4C3IL 4C3HL 3HJWB 3FKIL 1BRFA 2BE5D 5MFPA 1ZRPA 4Y52L 3B08B 1RWDA 1BQ8A 2E2JL 3LPEB 3RYGA 5M5XL 1LKMA 2Z3QB 4YWLA 2E2IL 1B2OA 3K35A 5JVG1 1VZGA 1S24A 2Y0SP 3LWOB 1TWGL 3KYXA 2NVYL 2Z3RB 1RDVA 4AHXA 3RZDL 5M5WL 1BFYA 1PFWA 1I3QL 1PFUA 5FJ8L 4BBSL 5MLC3 4X6AL 1FHMA 3H9CA 2XJQA 3S14L 3I4ML 1RB9A 4E6YA 3P2AA 1C09A 2YU9L 5MFZA 1I50L 1YUXA 4BY1L 3PIO1 2APOB 3H9BA 5IP7L 2DSXA 3HOYL 1S30A 1F4LA 5GADc 2HR5A 2MS3A 2M4YA 4A93L 1YV1A 4G6BA 1OWCA 2AQCA 4A3KL 4A3ML 3PKIA 2NVQL 1LTLA 4V196 4ZN3B 2VUML 1VZHA 2JA5L 7RXNA 3A44A 1H7VA 2K2DA 4AHYA 4TPUA 2JI3A 2M6PA 5GAGc 2XJSA 5AN9H 1RYQA 3JR7A 4BBRL 3RZTA 4AI2A 1B71A 1YK4A 3PL5A 1R0GA 4A3BL 3H99A 1NNQA 4A3IL 2JA6L 5GAEc 2AUSB 1DVBA 1SFOL 2PVEA 2PYAA 1TWFL 1SMUA 4AHZA 1NXEA 4AI3A 1VCXA 3GTQL 3CQZL 2PMZP 1E8JA 3HOZL 1IW7D 1OWBA 2A69D 3HKZP 4AI0A 1IU6A 2V3BB 1TWAL 2O5JD 3S2DL 1T9OA 3KYWA 2ERSA 3PZAA 3S1NL 2R93L 5C4JL 2JI2A 4B8CD 1YK5A 4QIWP 3GTLL 4BXXL 5RXNA 2RFKB 5EIOC 2JA7L 8RXNA 2NYDA 2ZIXA 3MSUA 3LWVB 3GTKL 1TWHL 1Z92B 3LWRB 3GTGL 3S15L 3SS2A 2CKCA 2A6HD 2CKAA 4AR3A 4A3CL 3KYVA 5FLML 4A3FL 4TVMA 1WCML 5MF6A 1LKOA 3GTPL 5C4XL 5DM61 1PFYA 3QVDA 4A3LL 2V0FA 1R0JA 3I4NL 1PZXA 4ZN1B 1IRNA 2AYJA 2GMGA 5H1Sc 1RYTA 2R7ZL 2C6AA 3QQCE 3K7AL 2VL6A 1IU5A 1S2ZA 4JAFA 1CADA 3PO3L 2M6OA 5IY0A 3S1QL 5C44L 4POGA 3S16L 3IU3I 1NXGA 5K2ME 1BQ9A 3S1ML 1R0HA 4POFA 5DM71 1R0FA 2NVTL 4U671 3GTOL 4WFN1 1B13A 2H12A 3KYYA 1RDGA 2WAQP 2XJPA 1B2JA 3J7Z1 3HOVL 3HOUL 5C3EL 4AYBP 3HJYB 3MQKB 1FHHA 4AR5A 1VZIA 1BE7A 1CAAA 2JA8L 2A68D 3KYUA 2EY4E 2B63L 3VPBE 2R92L 4A3DL 1Y1WL 4K9FA 3HAXC 3J7Y1 2QL0A 2B5ID 4AR6A 1PFVA 1QYBA 3LWQB 2HVYC 2KKDA 4ME3A 5IYDL 1P7PA 2L0ZA 2KN9A 2C6BA 1SMMA 5GAHc 4A3EL 1Y1VL 3M4OL 1T9QA 1R0IA 3S2HL 2A6ED 2XJTA 5AI2A 3H97A 4A3JL 2RDVA 2JI1A 1JYBA 4YWMA 3LWPB 3B0AB 1LKPA 4LHLA 3WWNB 1QCVA 5M3ML 3PO2L 3H3VM 3GTJL 2PPTA 3H0GL 2V0EA 1SMWA 1T9PA 3ZG6A 5IYBL 1DX8A 3PIP1 6RXNA 1ODHA 3WWLA 4XXBB 3PWFA 4GS7D 2E2HL 2PSMC 3S1RL 3M3YL 4AHWA 5AI3A 2XJVA 4AR4A 5IYCL 2XJUA 4C3JL 4Y7NL 1WJVA 4C2M1 3RZOL 3HOXL 1K83L 4AI1A 3RZ6A 2PVXA
chains in the Genus database with same CATH topology
1I6HL 2NVXL 2JA8L 2YU9L 1I50L 4BY7L 3S1NL 4BY1L 2B63L 2R93L 5C4JL 4QIWP 3GTLL 2R92L 3GTML 4BXXL 4A3DL 1Y1WL 5IP7L 3HOYL 2JA7L 4A93L 1R9TL 3GTKL 1TWHL 4A3KL 4A3ML 2NVQL 3GTGL 3S15L 4A3GL 2VUML 2JA5L 5IYDL 4A3CL 5FLML 3S17L 1TWCL 5M3FL 4A3FL 1WCML 4A3EL 3GTPL 5C4XL 1Y1VL 3M4OL 3HOWL 2WB1P 3S2HL 4BBRL 5IP9L 4A3LL 4A3JL 5M5YL 4C3IL 4C3HL 3I4NL 3FKIL 5M3ML 4A3BL 3PO2L 3H3VM 2R7ZL 4A3IL 4Y52L 3K7AL 3GTJL 2JA6L 2E2JL 3PO3L 1SFOL 3H0GL 3S1QL 5C44L 5M5XL 3S16L 1TWFL 2E2IL 3S1ML 5IYBL 2Y0SP 1TWGL 3GTQL 2NVYL 3CQZL 2NVTL 3GTOL 2PMZP 2E2HL 3HOZL 2WAQP 3RZDL 3S1RL 3M3YL 3HKZP 5M5WL 1I3QL 3HOVL 5IYCL 3HOUL 5C3EL 4AYBP 5FJ8L 4BBSL 1TWAL 4X6AL 3S2DL 4C3JL 4Y7NL 3RZOL 4C2M1 3HOXL 1K83L 3S14L 3I4ML
chains in the Genus database with same CATH homology


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