4A3EL

Rna polymerase ii initial transcribing complex with a 5nt dna-rna hybrid and soaked with ampcpp
Total Genus 2
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
2
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) }}
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 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 4a3eL00
3PO3L 3HOZL 3FKIL 3S17L 4A3LL 1TWGL 3S1ML 2NVXL 4A3EL 3HOVL 3GTGL 3I4NL 3HOXL 5M5XL 4QIWP 1K83L 3S1RL 5C4JL 4BBSL 5IP9L 4BBRL 4C3HL 3GTOL 2E2JL 3HOWL 2YU9L 5C44L 4A3GL 4X6AL 5M3ML 1TWAL 3GTKL 4A3DL 4A3JL 5IYBL 4Y7NL 2E2HL 3M4OL 2PMZP 1TWCL 5M5YL 1I3QL 2NVTL 3GTLL 2VUML 2WB1P 2B63L 3S2HL 2NVQL 3RZDL 1I50L 1TWHL 4BXXL 2E2IL 4A93L 3GTJL 3K7AL 4A3ML 3I4ML 2JA6L 5M3FL 3S14L 3HOUL 5IYCL 2R93L 1I6HL 2WAQP 4A3BL 2R92L 3S2DL 2Y0SP 2R7ZL 4C3IL 4BY1L 2JA8L 3PO2L 4BY7L 5IYDL 2JA5L 5FLML 4A3CL 3GTPL 3GTML 3S16L 4C2M1 1Y1VL 4AYBP 4Y52L 2NVYL 5FJ8L 1Y1WL 1TWFL 5C3EL 3S1NL 1R9TL 2JA7L 1WCML 3H0GL 4A3KL 3S15L 4A3IL 3M3YL 3RZOL 5C4XL 5IP7L 1SFOL 3GTQL 3CQZL 3HKZP 3HOYL 3S1QL 4A3FL 5M5WL 4C3JL 3H3VM
chains in the Genus database with same CATH superfamily
1YK5A 4UY81 1TWGL 3MSUA 1SMUA 1S24A 5M5XL 1RDGA 2Z3RB 4BBRL 3PIP1 2CKCA 4C3HL 1RYTA 4RXNA 5AI2A 2DSXA 2A6HD 2KKDA 1RWDA 2O5JD 5GAEc 3GTKL 3LWRB 2ERSA 3B0AB 2APOB 1LTLA 5RXNA 5GAGc 1RDVA 5M5YL 1R0HA 3ZG6A 2NVTL 2BE5D 1DX8A 1IROA 2WB1P 3LWPB 3S2HL 3PZAA 3KYXA 2XJQA 4GS7D 1S30A 4AR6A 3P2AA 1QCVA 5M3FL 4TVMA 5IYCL 2EY4E 2R93L 2JI2A 2WAQP 2R92L 4AI1A 2GMGA 3IU3I 2JA8L 3PO2L 3PWFA 4AI2A 1IW7D 5FLML 4A3CL 1IU6A 3GTML 1VZGA 3S16L 4C2M1 4AYBP 1F4LA 2C6BA 2NVYL 2M4YA 3H9BA 1SMMA 1YUXA 5C4XL 3LPEB 1PZXA 1PFWA 2H12A 3PKJA 1SFOL 3CQZL 5H1Sc 3H0GL 1BFYA 3H3VM 5DM71 3HOZL 5DM61 3S17L 3J7Y1 3H9CA 3S1ML 2NVXL 4K9FA 3HOVL 1PFVA 1YK4A 1T9OA 4QIWP 1K83L 3SS2A 1ZRPA 3LWQB 4AHYA 1RB9A 1BQ9A 3QVDA 1T9PA 2RDVA 3LWVB 3JR7A 2XJVA 3WWLA 5EIOC 2ZIXA 2C6AA 1TWAL 1JYBA 1NXGA 5K2ME 2PMZP 2XJUA 3NFPI 2PYAA 1I50L 2E2IL 1WJVA 3K7AL 2XJRA 2AYJA 4XGHA 3S14L 1DVBA 1I6HL 1YUZA 1P7PA 2AQCA 4LHNA 3S2DL 2Y0SP 2R7ZL 4C3IL 3J7Z1 4BY1L 1NXEA 4BY7L 5IYDL 2A6ED 3A44A 3HJWB 5GAHc 4YWMA 2M6OA 2ERJA 4Y52L 2V0EA 2JA7L 5AN9H 1YV1A 1PFUA 2AUSB 5MF6A 3M3YL 3RZOL 1VCXA 5IP7L 3KYWA 4YWLA 5IY0A 5MFZA 1RYQA 1B2OA 3PL5A 1CADA 4AHXA 1LKPA 3MQKB 4A3LL 2PVEA 4A3EL 2PVXA 2RFKB 3I4NL 3HOXL 4XXBB 2V3BB 7RXNA 1QYBA 1LKOA 3S1RL 2QL0A 2XJPA 4TPUA 5IP9L 2VL6A 1VZHA 3GTOL 2A68D 2E2JL 3RZTA 3HOWL 5C44L 4A3GL 4X6AL 5M3ML 4WFN1 4E6YA 1QQTA 5MFPA 4AHZA 5JVG1 4A3DL 5IYBL 2L0ZA 2NYDA 4JAEA 2PPTA 1I3QL 3GTLL 3RZDL 1R0FA 4ZN1B 2MS3A 3GTJL 1H7VA 5GADc 4A3ML 4POGA 3I4ML 4AR5A 2JA6L 2PSMC 2HVYC 4A3BL 1R0JA 3VPBE 4ZN3B 2JA5L 3HAXC 3GTPL 2K2DA 5MLC3 1E8JA 3QQCE 2LCQA 2JI1A 1Y1WL 1TWFL 1R9TL 4ME3A 1OWCA 2CR8A 4AHWA 1IRNA 1S2ZA 5AI3A 1SMWA 4AI0A 3HKZP 3S1QL 3KYUA 1OWBA 2KN9A 1B2JA 3FDJA 4JAFA 3PO3L 3FKIL 3K35A 1PFYA 1R0GA 4JADA 1IU5A 1T9QA 3GTGL 1BE7A 2XJTA 3LWOB 5C4JL 4BBSL 3RZ6A 3B08B 3H99A 1R0IA 4LHLA 4AR4A 2XJSA 3RYGA 2YU9L 2Z3QB 3HJYB 2HR5A 6RXNA 1VZIA 5MGNA 4A3JL 1BQ8A 4Y7NL 2E2HL 3M4OL 3KYVA 3LNLA 1TWCL 2M4VA 1CAAA 2J9UB 2VUML 2B63L 2NVQL 1TWHL 4BXXL 4A93L 1C09A 4AI3A 1ODHA 4V196 8RXNA 1LKMA 1NNQA 4U671 2B5ID 3HOUL 3KYYA 4G6BA 2JI3A 5JVH1 1FHHA 3MPSA 5EINC 1BRFA 2V0FA 3PKIA 2CKAA 1B13A 1Y1VL 1FHMA 3PIO1 5FJ8L 5C3EL 3S1NL 1WCML 1Z92B 4JAGA 4AR3A 2A69D 4A3KL 3S15L 4A3IL 3H97A 3P8BA 4B8CD 1B71A 3GTQL 3HOYL 2M6PA 4POFA 4A3FL 5M5WL 3WWNB 4C3JL
chains in the Genus database with same CATH topology
3PO3L 3HOZL 3FKIL 3S17L 4A3LL 1TWGL 3S1ML 2NVXL 4A3EL 3HOVL 3GTGL 3I4NL 3HOXL 5M5XL 4QIWP 1K83L 3S1RL 5C4JL 4BBSL 5IP9L 4BBRL 4C3HL 3GTOL 2E2JL 3HOWL 2YU9L 5C44L 4A3GL 4X6AL 5M3ML 1TWAL 3GTKL 4A3DL 4A3JL 5IYBL 4Y7NL 2E2HL 3M4OL 2PMZP 1TWCL 5M5YL 1I3QL 2NVTL 3GTLL 2VUML 2WB1P 2B63L 3S2HL 2NVQL 3RZDL 1I50L 1TWHL 4BXXL 2E2IL 4A93L 3GTJL 3K7AL 4A3ML 3I4ML 2JA6L 5M3FL 3S14L 3HOUL 5IYCL 2R93L 1I6HL 2WAQP 4A3BL 2R92L 3S2DL 2Y0SP 2R7ZL 4C3IL 4BY1L 2JA8L 3PO2L 4BY7L 5IYDL 2JA5L 5FLML 4A3CL 3GTPL 3GTML 3S16L 4C2M1 1Y1VL 4AYBP 4Y52L 2NVYL 5FJ8L 1Y1WL 1TWFL 5C3EL 3S1NL 1R9TL 2JA7L 1WCML 3H0GL 4A3KL 3S15L 4A3IL 3M3YL 3RZOL 5C4XL 5IP7L 1SFOL 3GTQL 3CQZL 3HKZP 3HOYL 3S1QL 4A3FL 5M5WL 4C3JL 3H3VM
chains in the Genus database with same CATH homology


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