4A3JL

Rna polymerase ii initial transcribing complex with a 2nt dna-rna hybrid and soaked with gmpcpp
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 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 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 4a3jL00
3S2HL 4Y7NL 3GTPL 5IP7L 4BY1L 2NVQL 2WB1P 3S2DL 2NVYL 1K83L 3GTQL 3HOXL 5IYCL 4BBSL 1TWAL 1TWHL 4C3IL 4A3LL 4A93L 2VUML 2JA7L 3H0GL 3M4OL 2Y0SP 3S14L 3S1RL 4A3EL 1I6HL 5C3EL 4AYBP 1Y1WL 5M5WL 1TWCL 2NVTL 5M5YL 2YU9L 3S16L 3PO3L 2R92L 5IYBL 2B63L 4X6AL 3FKIL 4A3GL 1I3QL 3GTJL 1I50L 3HOVL 3PO2L 2JA5L 3HKZP 3HOWL 5IP9L 5C4XL 1Y1VL 2WAQP 3GTLL 2R93L 3CQZL 4C2M1 3S1NL 1SFOL 5FLML 4A3JL 1R9TL 2JA6L 2E2HL 2PMZP 4A3ML 5M5XL 2NVXL 3S1QL 5C4JL 3GTOL 4BXXL 3H3VM 2E2IL 3S15L 3RZDL 2E2JL 3GTKL 3S1ML 2R7ZL 3I4NL 4A3DL 4BBRL 1TWFL 3HOUL 5IYDL 3HOZL 5M3ML 3HOYL 3GTML 4A3FL 2JA8L 5C44L 3RZOL 4C3HL 4QIWP 4A3CL 5M3FL 4Y52L 3K7AL 4A3BL 5FJ8L 3GTGL 1TWGL 4A3IL 4A3KL 4BY7L 4C3JL 3I4ML 1WCML 3M3YL 3S17L
chains in the Genus database with same CATH superfamily
4Y7NL 5IP7L 4AR6A 2WB1P 1S2ZA 5EINC 3S2DL 3PIP1 2J9UB 5AI2A 5IYCL 1TWAL 2AUSB 4AR4A 3H97A 4ME3A 1WJVA 4JAGA 3KYYA 2JA7L 4UY81 2K2DA 2VL6A 3S1RL 2KN9A 4A3EL 1R0FA 4G6BA 5M5WL 3LWOB 2JI2A 2XJUA 1NXEA 3NFPI 1SMWA 3MQKB 5M5YL 1VZIA 2O5JD 4POGA 1I50L 4RXNA 2BE5D 2JA5L 3HKZP 1IROA 5IP9L 2NYDA 1RDGA 3WWLA 2R93L 4AHWA 1IRNA 3QQCE 3H99A 1SMUA 1SFOL 5MFPA 4AHZA 2A68D 2NVXL 3HJYB 1IU5A 3GTKL 4AI1A 4B8CD 5GAEc 1SMMA 2Z3RB 3VPBE 4AHYA 3PIO1 5DM71 3HOUL 2L0ZA 5M3ML 2KKDA 1B13A 2PVXA 3HOYL 5C44L 1IU6A 5H1Sc 3PWFA 1T9OA 2A69D 1ODHA 4Y52L 1DX8A 4A3IL 2ERJA 5EIOC 1WCML 2EY4E 4TVMA 3M3YL 3S17L 3S2HL 5MGNA 4U671 4BY1L 3A44A 1BRFA 1K83L 3PL5A 2QL0A 1TWHL 8RXNA 6RXNA 1PFVA 3H9CA 3LWQB 1YK4A 1R0HA 3QVDA 4YWLA 3K35A 1C09A 3P8BA 2AYJA 4XXBB 2XJTA 5C3EL 4AYBP 2V3BB 1ZRPA 3LWVB 1VCXA 5JVH1 3S16L 1YUZA 4JAFA 1OWCA 4A3GL 1IW7D 4ZN1B 1YUXA 3GTJL 5JVG1 1CAAA 2M4YA 1CADA 2M6OA 5DM61 3J7Y1 2JI1A 1LTLA 1Y1VL 2GMGA 4C2M1 2A6ED 1R9TL 2E2HL 4JAEA 4YWMA 5K2ME 3GTOL 3KYVA 2PVEA 1T9PA 3S15L 1LKMA 3RZDL 2E2JL 3HAXC 3S1ML 2PPTA 2R7ZL 1BE7A 2RDVA 3I4NL 4A3DL 3J7Z1 4BBRL 5IYDL 2DSXA 1R0IA 3GTML 4A3FL 5GAGc 2JA8L 1DVBA 1PFUA 4WFN1 2M6PA 5GAHc 3GTGL 2XJSA 2M4VA 4A3KL 4BY7L 3I4ML 1BFYA 5MFZA 1BQ9A 3GTPL 4AI2A 1E8JA 3FDJA 2XJQA 2NVQL 4AI0A 1RYQA 4K9FA 1PFYA 4C3IL 4A3LL 4A93L 3LNLA 1S24A 1NXGA 2APOB 1B71A 2V0EA 2XJRA 3M4OL 2Y0SP 1I6HL 1R0GA 1H7VA 2JI3A 4LHNA 1TWCL 2NVTL 3MSUA 2YU9L 3PKJA 3PO3L 2B63L 4X6AL 1I3QL 3RZTA 1Z92B 1VZHA 3HOWL 2CR8A 4AI3A 1JYBA 5C4XL 3CQZL 2MS3A 3S1NL 1FHMA 2AQCA 1B2OA 5FLML 1QQTA 1OWBA 5M5XL 5C4JL 1LKOA 3H3VM 2E2IL 1QYBA 1F4LA 3SS2A 4AR3A 4LHLA 1R0JA 2HR5A 2C6BA 1VZGA 1LKPA 2HVYC 2LCQA 1BQ8A 5AN9H 2XJPA 3HOZL 3H9BA 2RFKB 4ZN3B 3ZG6A 3KYUA 4TPUA 4C3HL 4A3CL 5M3FL 1YK5A 3JR7A 4A3BL 2H12A 2ZIXA 1QCVA 1RDVA 7RXNA 1TWGL 2Z3QB 2CKCA 5GADc 5MF6A 1FHHA 4V196 2NVYL 3IU3I 4XGHA 1S30A 3LWPB 3GTQL 1P7PA 3KYXA 1B2JA 3HOXL 2C6AA 4BBSL 2VUML 5MLC3 5RXNA 3LWRB 3H0GL 1RYTA 3S14L 1Y1WL 2CKAA 3LPEB 3HJWB 2V0FA 4E6YA 3RZ6A 5AI3A 2PSMC 4GS7D 1NNQA 2R92L 5IYBL 3FKIL 3PKIA 4JADA 4AHXA 3WWNB 1PZXA 3HOVL 3PO2L 3MPSA 3RYGA 3PZAA 1RB9A 2WAQP 3GTLL 5IY0A 4A3JL 2JA6L 1YV1A 2PMZP 4A3ML 3S1QL 4BXXL 3B08B 2PYAA 2A6HD 2B5ID 1TWFL 3P2AA 3B0AB 1PFWA 2XJVA 3KYWA 3RZOL 4AR5A 4QIWP 4POFA 3K7AL 2ERSA 1RWDA 5FJ8L 4C3JL 1T9QA
chains in the Genus database with same CATH topology
3S2HL 4Y7NL 3GTPL 5IP7L 4BY1L 2NVQL 2WB1P 3S2DL 2NVYL 1K83L 3GTQL 3HOXL 5IYCL 4BBSL 1TWAL 1TWHL 4C3IL 4A3LL 4A93L 2VUML 2JA7L 3H0GL 3M4OL 2Y0SP 3S14L 3S1RL 4A3EL 1I6HL 5C3EL 4AYBP 1Y1WL 5M5WL 1TWCL 2NVTL 5M5YL 2YU9L 3S16L 3PO3L 2R92L 5IYBL 2B63L 4X6AL 3FKIL 4A3GL 1I3QL 3GTJL 1I50L 3HOVL 3PO2L 2JA5L 3HKZP 3HOWL 5IP9L 5C4XL 1Y1VL 2WAQP 3GTLL 2R93L 3CQZL 4C2M1 3S1NL 1SFOL 5FLML 4A3JL 1R9TL 2JA6L 2E2HL 2PMZP 4A3ML 5M5XL 2NVXL 3S1QL 5C4JL 3GTOL 4BXXL 3H3VM 2E2IL 3S15L 3RZDL 2E2JL 3GTKL 3S1ML 2R7ZL 3I4NL 4A3DL 4BBRL 1TWFL 3HOUL 5IYDL 3HOZL 5M3ML 3HOYL 3GTML 4A3FL 2JA8L 5C44L 3RZOL 4C3HL 4QIWP 4A3CL 5M3FL 4Y52L 3K7AL 4A3BL 5FJ8L 3GTGL 1TWGL 4A3IL 4A3KL 4BY7L 4C3JL 3I4ML 1WCML 3M3YL 3S17L
chains in the Genus database with same CATH homology


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