3S1NL

Rna polymerase ii initiation complex with a 5-nt rna (variant 2)
Total Genus 3
Loading diagram...

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
3
sequence length
46
structure length
46
Chain Sequence
ATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
publication title Initiation complex structure and promoter proofreading.
pubmed doi rcsb
molecule tags Transcription/rna/dna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
total genus 3
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2011-05-15

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 3s1nL00
1TWGL 3HOVL 4A3CL 4A3KL 3HOUL 1TWAL 2E2JL 1I3QL 1K83L 5IYDL 3M4OL 3GTQL 5M5XL 1Y1VL 1Y1WL 2E2HL 1SFOL 3S15L 3H3VM 2JA8L 4A3FL 3S2DL 2VUML 3S1ML 4A3EL 4BXXL 2JA6L 2NVYL 3GTLL 4C2M1 1WCML 3S17L 2YU9L 2R93L 5C3EL 3S1NL 3GTPL 4QIWP 5IP9L 3HOZL 2NVQL 1TWFL 5IP7L 2NVTL 3M3YL 1I6HL 5IYCL 4BBSL 2E2IL 4A93L 4A3GL 2R7ZL 3H0GL 5C44L 4BY7L 5FLML 5M5WL 4A3JL 3K7AL 1TWCL 3GTGL 3GTOL 4C3HL 3GTJL 3GTML 3CQZL 3S16L 4A3ML 3HKZP 5C4XL 3HOXL 1I50L 3I4ML 3I4NL 5M3FL 2B63L 3HOYL 2NVXL 2WB1P 4BY1L 3S1RL 2R92L 4A3IL 5C4JL 3S14L 5M3ML 4C3IL 2WAQP 3PO3L 2JA7L 4BBRL 4A3BL 4X6AL 3HOWL 5FJ8L 3S2HL 4AYBP 2JA5L 1R9TL 4Y52L 2Y0SP 1TWHL 3PO2L 5M5YL 3RZOL 3GTKL 4Y7NL 3RZDL 4C3JL 2PMZP 3S1QL 4A3DL 3FKIL 4A3LL 5IYBL
chains in the Genus database with same CATH superfamily
3MPSA 1BRFA 2B5ID 1QCVA 2E2JL 2E2HL 1SFOL 4JAEA 3S15L 2JA8L 4A3FL 2RDVA 1LTLA 1IU6A 5EINC 3S1ML 3WWNB 2L0ZA 2JA6L 2NVYL 2DSXA 1H7VA 3LWQB 1CAAA 2CKAA 5C3EL 4YWLA 3S1NL 4XXBB 2NVTL 1DX8A 2PSMC 3M3YL 2XJQA 3FDJA 3B08B 1VZGA 2AQCA 2BE5D 4AHZA 4A3JL 3K7AL 3GTJL 2NYDA 5MF6A 5DM71 1RB9A 3PWFA 2B63L 1B13A 4BY1L 4AHYA 2XJRA 2M6PA 4AHXA 5C4JL 2XJSA 3LWVB 1LKMA 1Z92B 2XJUA 2A69D 4AI1A 1R0GA 2JI2A 4WFN1 3HJWB 1R9TL 1PZXA 3H9BA 3KYWA 1RWDA 4ME3A 2Y0SP 3K35A 1VZHA 1RDGA 5H1Sc 3RZDL 1OWBA 2PMZP 3S1QL 3FKIL 3VPBE 1TWGL 3HOVL 4A3CL 1RYTA 5IY0A 4A3KL 1LKOA 2VL6A 4JAGA 3MSUA 3PIP1 1C09A 1PFUA 4BXXL 3GTLL 3H9CA 4C2M1 1WCML 3S17L 1BFYA 5JVH1 5JVG1 5IP9L 2NVQL 1T9PA 2V0FA 4V196 3P8BA 5AN9H 3HJYB 1F4LA 2A6ED 1PFVA 1T9QA 5C44L 1S2ZA 5FLML 1DVBA 3GTOL 4C3HL 3GTML 3LNLA 5DM61 3S16L 4A3ML 1QYBA 4TVMA 2Z3RB 3LWOB 3HOYL 2PVXA 1IW7D 3H99A 2JI3A 5MLC3 3H97A 2R92L 4JADA 3S14L 1PFYA 2H12A 1PFWA 4C3IL 2WAQP 1IROA 2O5JD 4BBRL 4E6YA 2ERSA 1FHMA 1IU5A 5MFPA 5FJ8L 4B8CD 3QQCE 2JA5L 1SMUA 2AYJA 4AI0A 1B71A 1BE7A 4C3JL 2HVYC 2MS3A 2HR5A 3PIO1 1R0IA 7RXNA 1TWAL 4AR4A 1B2JA 1I3QL 1R0FA 5IYDL 3M4OL 3GTQL 5M5XL 1YUZA 3IU3I 1Y1WL 1JYBA 1CADA 3HAXC 1WJVA 2ERJA 3NFPI 3S2DL 2VUML 1YK5A 4A3EL 2PPTA 2K2DA 2R93L 4AR5A 4QIWP 5AI3A 2GMGA 6RXNA 4AI2A 5GAEc 2Z3QB 2XJVA 1I6HL 5IYCL 1BQ8A 4YWMA 4BBSL 4XGHA 2A6HD 3KYYA 2V0EA 3B0AB 2AUSB 1R0JA 2RFKB 3H0GL 5M5WL 1P7PA 5MFZA 2CKCA 2M4VA 3CQZL 1YK4A 3HOXL 3I4ML 5RXNA 4LHNA 5M3FL 4AI3A 2NVXL 1IRNA 8RXNA 2WB1P 5GADc 1NXGA 2C6BA 5M3ML 1FHHA 4UY81 2M6OA 2V3BB 4A3BL 2KKDA 2CR8A 3QVDA 4X6AL 3HOWL 3PKIA 4AYBP 3S2HL 1YV1A 4LHLA 1NXEA 3PO2L 5M5YL 1B2OA 3PZAA 3RZOL 3KYVA 4A3DL 3LWPB 1ZRPA 1VZIA 4POFA 2EY4E 3HOUL 3ZG6A 1K83L 1E8JA 4ZN3B 1Y1VL 1S30A 2C6AA 1R0HA 3H3VM 1T9OA 2PVEA 4G6BA 5MGNA 3RZTA 4U671 2YU9L 1S24A 3J7Z1 3GTPL 4AHWA 3HOZL 2JI1A 1LKPA 1RDVA 1TWFL 5IP7L 2XJTA 5GAHc 3PKJA 3LWRB 4RXNA 2E2IL 5AI2A 4AR3A 3LPEB 3P2AA 1VCXA 4A93L 4POGA 4A3GL 2APOB 2R7ZL 4BY7L 1SMWA 4ZN1B 1TWCL 3GTGL 3RYGA 3A44A 2M4YA 3JR7A 4TPUA 3HKZP 3J7Y1 5C4XL 1I50L 5EIOC 3I4NL 3KYUA 3SS2A 5GAGc 1YUXA 1BQ9A 4K9FA 3S1RL 3RZ6A 4A3IL 3PL5A 2PYAA 1QQTA 3KYXA 3PO3L 3MQKB 2JA7L 2QL0A 1ODHA 4AR6A 2A68D 2LCQA 4Y52L 1OWCA 5K2ME 1TWHL 3GTKL 3WWLA 4Y7NL 2ZIXA 2KN9A 1NNQA 2XJPA 4GS7D 1RYQA 4JAFA 4A3LL 1SMMA 5IYBL 2J9UB
chains in the Genus database with same CATH topology
1TWGL 3HOVL 4A3CL 4A3KL 3HOUL 1TWAL 2E2JL 1I3QL 1K83L 5IYDL 3M4OL 3GTQL 5M5XL 1Y1VL 1Y1WL 2E2HL 1SFOL 3S15L 3H3VM 2JA8L 4A3FL 3S2DL 2VUML 3S1ML 4A3EL 4BXXL 2JA6L 2NVYL 3GTLL 4C2M1 1WCML 3S17L 2YU9L 2R93L 5C3EL 3S1NL 3GTPL 4QIWP 5IP9L 3HOZL 2NVQL 1TWFL 5IP7L 2NVTL 3M3YL 1I6HL 5IYCL 4BBSL 2E2IL 4A93L 4A3GL 2R7ZL 3H0GL 5C44L 4BY7L 5FLML 5M5WL 4A3JL 3K7AL 1TWCL 3GTGL 3GTOL 4C3HL 3GTJL 3GTML 3CQZL 3S16L 4A3ML 3HKZP 5C4XL 3HOXL 1I50L 3I4ML 3I4NL 5M3FL 2B63L 3HOYL 2NVXL 2WB1P 4BY1L 3S1RL 2R92L 4A3IL 5C4JL 3S14L 5M3ML 4C3IL 2WAQP 3PO3L 2JA7L 4BBRL 4A3BL 4X6AL 3HOWL 5FJ8L 3S2HL 4AYBP 2JA5L 1R9TL 4Y52L 2Y0SP 1TWHL 3PO2L 5M5YL 3RZOL 3GTKL 4Y7NL 3RZDL 4C3JL 2PMZP 3S1QL 4A3DL 3FKIL 4A3LL 5IYBL
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...