3RZDL

Rna polymerase ii initiation complex with a 5-nt rna
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 Initiation complex structure and promoter proofreading.
pubmed doi rcsb
molecule tags Transcription/rna/dna
total genus 2
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2011-05-11

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 3rzdL00
4A3JL 3HOZL 3FKIL 1TWFL 3GTGL 5M5YL 2NVXL 5IP7L 1TWGL 4A93L 2NVTL 3CQZL 3PO3L 3S1QL 2JA5L 2JA8L 3S2HL 5IYBL 3GTPL 3HOWL 2R93L 3M4OL 2PMZP 2VUML 3HOVL 4AYBP 1SFOL 3S17L 4BY7L 2JA6L 4Y52L 4C3HL 3S2DL 4C3JL 4QIWP 4BBSL 5FLML 3HOYL 4A3DL 3I4ML 4BXXL 4A3ML 4C3IL 4A3IL 3K7AL 1I3QL 5C3EL 4A3FL 2E2IL 4BY1L 2R7ZL 4A3LL 2E2JL 5M5WL 5C44L 3GTQL 3S16L 1R9TL 3S1NL 2E2HL 2Y0SP 4A3EL 3HKZP 2JA7L 3RZOL 2R92L 2WB1P 1TWHL 3S1RL 5M5XL 5C4JL 5C4XL 5IYCL 5M3ML 1I6HL 4A3CL 5IP9L 3S1ML 1Y1VL 4A3KL 3S15L 3H0GL 3GTLL 3S14L 3HOUL 2B63L 3GTML 2NVYL 2WAQP 4BBRL 1Y1WL 5IYDL 1TWAL 2YU9L 1I50L 5M3FL 1K83L 4A3GL 3RZDL 1WCML 3GTOL 3HOXL 3GTKL 3PO2L 1TWCL 4Y7NL 3I4NL 4A3BL 3H3VM 4X6AL 5FJ8L 3GTJL 2NVQL 4C2M1 3M3YL
chains in the Genus database with same CATH superfamily
1RB9A 3FKIL 2NVXL 1VZHA 2HVYC 2NVTL 3S1QL 4U671 1S30A 3PZAA 2JA8L 5GAEc 3MPSA 4LHLA 3H97A 1R0IA 3M4OL 2APOB 4UY81 2Z3RB 1BQ8A 3HOVL 3PWFA 4Y52L 2AYJA 1CADA 1S2ZA 3H9CA 2LCQA 3S2DL 3I4ML 4C3IL 4V196 4A3FL 4BY1L 2E2IL 5M5WL 1P7PA 3GTQL 3S16L 4JAGA 1RYTA 2JA7L 2C6AA 3J7Z1 3RZOL 1TWHL 4E6YA 1PFWA 4AR4A 1BRFA 4ME3A 1QYBA 5MGNA 3HAXC 1LKOA 5AN9H 5IP9L 3S1ML 3P2AA 1YUXA 1C09A 4A3KL 4YWMA 4AHWA 3GTLL 3S14L 2B63L 1IROA 2WAQP 5AI2A 4ZN3B 1FHHA 4AI3A 2KKDA 2PVEA 4AHXA 1K83L 3RZ6A 3H9BA 3GTKL 2V0FA 2A69D 4JADA 1BFYA 6RXNA 2CKAA 1NXEA 2M4VA 1SMUA 2ERJA 3PKJA 1H7VA 1PFYA 5GAHc 4A3JL 3HOZL 1F4LA 2M6PA 5GAGc 1TWFL 3GTGL 2MS3A 1NXGA 3CQZL 3WWNB 4AR5A 2V0EA 1BE7A 2HR5A 2XJTA 2QL0A 2R93L 2PMZP 1T9OA 4B8CD 3VPBE 2XJUA 2RDVA 1SFOL 3PIO1 3SS2A 4TPUA 1BQ9A 5K2ME 5JVH1 1YK5A 2L0ZA 2DSXA 1JYBA 3LNLA 4QIWP 4BXXL 1DX8A 1CAAA 2R7ZL 2E2JL 2AUSB 4AR6A 3HJYB 3HKZP 4WFN1 2WB1P 2GMGA 3KYXA 3MSUA 5M5XL 5C4JL 5C4XL 1B71A 2XJPA 5IYCL 3LWVB 1RYQA 1S24A 2ZIXA 5DM61 3H0GL 3HOUL 3GTML 1Y1WL 5IYDL 2VL6A 1I50L 3J7Y1 2A68D 2JI3A 4JAEA 5EINC 3QVDA 4A3GL 5RXNA 3LWQB 1R0FA 3PO2L 7RXNA 3H3VM 1QCVA 3PKIA 2ERSA 3GTJL 3KYVA 2V3BB 1OWCA 2JI1A 4C2M1 3K35A 1R0HA 2PVXA 1YV1A 4A93L 2JA5L 2JI2A 3KYYA 3HOWL 3MQKB 4XGHA 3NFPI 1ODHA 3S17L 4BY7L 4C3HL 4BBSL 3HOYL 4POFA 4A3ML 3LWRB 4A3IL 3K7AL 1I3QL 1T9PA 5C44L 1R9TL 1VCXA 3B08B 3S1NL 4A3EL 2XJVA 2O5JD 1LKPA 1WJVA 2AQCA 1LKMA 3S1RL 2NYDA 3LWPB 1R0GA 1PFUA 3IU3I 3PIP1 2A6ED 5M3ML 4A3CL 1ZRPA 2J9UB 3KYUA 1FHMA 2RFKB 2NVYL 5MF6A 4BBRL 4XXBB 3H99A 2K2DA 5M3FL 3RZDL 1RWDA 4A3BL 5IY0A 3RZTA 4AI2A 5H1Sc 2C6BA 2CKCA 4JAFA 2PYAA 3M3YL 3P8BA 3WWLA 2A6HD 4RXNA 5M5YL 5IP7L 4YWLA 1TWGL 2H12A 3PO3L 4AI1A 1NNQA 5AI3A 2PSMC 4LHNA 1R0JA 5MFZA 3S2HL 5IYBL 5EIOC 3GTPL 4AI0A 2KN9A 2Z3QB 3LPEB 4K9FA 2VUML 3HJWB 4AHZA 1LTLA 2CR8A 4G6BA 2M4YA 3KYWA 4AYBP 5MFPA 1B2JA 2JA6L 2BE5D 4C3JL 2XJRA 5FLML 2B5ID 5GADc 4A3DL 3QQCE 5C3EL 4A3LL 3JR7A 5DM71 4TVMA 2M6OA 2E2HL 2Y0SP 2EY4E 1SMWA 1B13A 4POGA 1OWBA 1RDVA 2R92L 3ZG6A 1PFVA 1SMMA 1B2OA 1VZGA 1QQTA 8RXNA 1I6HL 3LWOB 1Y1VL 1IW7D 1PZXA 1RDGA 2PPTA 3S15L 1VZIA 2XJQA 3FDJA 1YUZA 1IRNA 3PL5A 4GS7D 1TWAL 1T9QA 2YU9L 5JVG1 5MLC3 3B0AB 4AHYA 1WCML 3RYGA 3GTOL 3HOXL 4AR3A 4ZN1B 1YK4A 3A44A 1E8JA 1TWCL 4Y7NL 3I4NL 4X6AL 1DVBA 2XJSA 5FJ8L 1IU5A 1Z92B 1IU6A 2NVQL
chains in the Genus database with same CATH topology
4A3JL 3HOZL 3FKIL 1TWFL 3GTGL 5M5YL 2NVXL 5IP7L 1TWGL 4A93L 2NVTL 3CQZL 3PO3L 3S1QL 2JA5L 2JA8L 3S2HL 5IYBL 3GTPL 3HOWL 2R93L 3M4OL 2PMZP 2VUML 3HOVL 4AYBP 1SFOL 3S17L 4BY7L 2JA6L 4Y52L 4C3HL 3S2DL 4C3JL 4QIWP 4BBSL 5FLML 3HOYL 4A3DL 3I4ML 4BXXL 4A3ML 4C3IL 4A3IL 3K7AL 1I3QL 5C3EL 4A3FL 2E2IL 4BY1L 2R7ZL 4A3LL 2E2JL 5M5WL 5C44L 3GTQL 3S16L 1R9TL 3S1NL 2E2HL 2Y0SP 4A3EL 3HKZP 2JA7L 3RZOL 2R92L 2WB1P 1TWHL 3S1RL 5M5XL 5C4JL 5C4XL 5IYCL 5M3ML 1I6HL 4A3CL 5IP9L 3S1ML 1Y1VL 4A3KL 3S15L 3H0GL 3GTLL 3S14L 3HOUL 2B63L 3GTML 2NVYL 2WAQP 4BBRL 1Y1WL 5IYDL 1TWAL 2YU9L 1I50L 5M3FL 1K83L 4A3GL 3RZDL 1WCML 3GTOL 3HOXL 3GTKL 3PO2L 1TWCL 4Y7NL 3I4NL 4A3BL 3H3VM 4X6AL 5FJ8L 3GTJL 2NVQL 4C2M1 3M3YL
chains in the Genus database with same CATH homology


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