4A3CL

Rna polymerase ii initial transcribing complex with a 5nt dna-rna hybrid
Total Genus 1
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
1
sequence length
46
structure length
46
Chain Sequence
b'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 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 4a3cL00
5FJ8L 3GTKL 3S17L 5IYDL 2R93L 5C3EL 1TWCL 2E2JL 3S2DL 1I6HL 3S1ML 4A3LL 3M4OL 2NVQL 3PO2L 3M3YL 4X6AL 4A3KL 4A3CL 2JA7L 2JA8L 5IYBL 3H3VM 5IP7L 4A93L 3K7AL 2JA6L 4C2M1 3HOWL 1I3QL 3GTJL 5C44L 4BBSL 2JA5L 3CQZL 3PO3L 3FKIL 4A3IL 4Y52L 2E2HL 1TWHL 3GTOL 3HOZL 2R7ZL 1WCML 1TWAL 4A3FL 1Y1WL 4A3GL 5C4JL 1K83L 5M5WL 3RZDL 4C3JL 4BY1L 2R92L 4A3DL 4A3BL 2WAQP 3GTQL 1TWFL 4A3JL 2PMZP 2YU9L 3RZOL 5M3FL 3GTGL 3GTLL 2B63L 1TWGL 3S2HL 1Y1VL 4AYBP 3S14L 2E2IL 4BBRL 3S16L 1SFOL 2Y0SP 4QIWP 5M5YL 1R9TL 5FLML 2VUML 4BXXL 4Y7NL 5M3ML 3HOUL 5M5XL 3GTPL 3HOYL 5C4XL 3HKZP 3S15L 2NVTL 3GTML 3HOVL 3HOXL 3S1NL 2NVYL 3S1QL 5IP9L 4C3HL 2WB1P 4A3EL 4A3ML 4C3IL 3I4ML 3S1RL 3H0GL 2NVXL 5IYCL 4BY7L 1I50L 3I4NL
chains in the Genus database with same CATH superfamily
2K2DA 1R0FA 3GTKL 1R0JA 3MSUA 1VZIA 1TWCL 1R0HA 2E2JL 5MFPA 1S30A 3S1ML 1RDVA 2M4VA 3M4OL 5JVG1 2AUSB 2XJUA 3H99A 1B13A 1OWBA 5IY0A 3LWPB 1T9OA 4ME3A 1ZRPA 2JI2A 3SS2A 1RB9A 3PKJA 5DM71 1R0IA 2JA6L 1IW7D 2A69D 3HOWL 1I3QL 5C44L 2A6HD 5MGNA 3FKIL 1SMWA 4AR4A 2R7ZL 2PSMC 1WCML 3LNLA 3WWLA 1PFWA 1B71A 5EIOC 3RZ6A 2Z3RB 3MQKB 2V0EA 2BE5D 2WAQP 5JVH1 3GTQL 2PMZP 1CADA 2AQCA 2YU9L 3RZOL 1IRNA 3GTGL 4POGA 3KYYA 4U671 4ZN3B 4AHZA 4BBRL 5GAEc 3VPBE 5MF6A 1C09A 1DVBA 4YWMA 4BXXL 4B8CD 1PFUA 3HOUL 5M5XL 1VZGA 2RDVA 2NVTL 3PZAA 1JYBA 2O5JD 1FHMA 3HOXL 3WWNB 4GS7D 3S1NL 2XJVA 3HAXC 1FHHA 1R0GA 3LWRB 3S1RL 1BQ8A 1WJVA 2M6OA 1VCXA 5IYCL 1F4LA 3ZG6A 2KN9A 2LCQA 3PKIA 2V0FA 3S17L 5IYDL 2XJQA 2NVQL 3PO2L 4ZN1B 4X6AL 4A3KL 5MFZA 2JA7L 1QQTA 1SMUA 5IP7L 2XJRA 2XJSA 3K7AL 1S24A 4AR3A 3GTJL 5AI2A 4BBSL 2JA5L 1B2JA 3CQZL 1LKMA 4A3IL 4Y52L 5AI3A 2EY4E 2PVEA 4A3GL 1RYTA 5C4JL 1K83L 4BY1L 4JADA 3LPEB 3LWVB 3KYWA 2QL0A 1T9QA 4XGHA 4AI0A 1RWDA 5M3FL 3IU3I 3P2AA 3K35A 1TWGL 1YK5A 1Y1VL 1SMMA 4AYBP 3A44A 2E2IL 2HVYC 5GAGc 5M5YL 2XJTA 4Y7NL 1LKOA 1E8JA 4JAGA 3S15L 1LKPA 3GTML 1NNQA 1PZXA 1IU5A 4C3HL 4AHXA 3H0GL 2RFKB 4JAFA 2GMGA 2VL6A 1VZHA 3QQCE 2Z3QB 1I50L 5RXNA 3PIP1 3J7Y1 1BE7A 5FJ8L 5C3EL 1I6HL 4A3LL 3KYVA 3M3YL 4A3CL 5IYBL 2CR8A 4A93L 3MPSA 4LHLA 1CAAA 1BFYA 3PO3L 2MS3A 2E2HL 1PFYA 3JR7A 1RYQA 1TWHL 4AR5A 1NXEA 5GAHc 5GADc 4A3FL 2B5ID 1Y1WL 4XXBB 5DM61 4POFA 2JI1A 1YK4A 5M5WL 3FDJA 1IU6A 4V196 2R92L 4A3BL 3J7Z1 1IROA 3RYGA 2L0ZA 4WFN1 2PVXA 3H97A 1NXGA 1P7PA 3B0AB 4G6BA 3GTLL 2NYDA 3HJWB 1YUZA 4AR6A 3S16L 2A6ED 4QIWP 1R9TL 2AYJA 2VUML 3LWOB 2ZIXA 2ERJA 5M3ML 4AI3A 5EINC 5K2ME 3GTPL 3HOYL 7RXNA 2V3BB 4RXNA 3QVDA 2CKAA 3P8BA 4YWLA 1BRFA 5IP9L 2WB1P 4C3IL 4UY81 4AI1A 2NVXL 1QYBA 2DSXA 1YUXA 1H7VA 2APOB 4BY7L 6RXNA 2PPTA 2HR5A 1BQ9A 5H1Sc 2J9UB 2M4YA 2R93L 3S2DL 4AHWA 3H9BA 5AN9H 1DX8A 2A68D 4TPUA 3HJYB 2JA8L 3H3VM 2KKDA 2XJPA 4TVMA 1B2OA 8RXNA 3B08B 4C2M1 2ERSA 1LTLA 1ODHA 2C6AA 4AI2A 1Z92B 3HOZL 3GTOL 1S2ZA 1TWAL 2M6PA 2H12A 3RZDL 4C3JL 4A3DL 1OWCA 1QCVA 1TWFL 4A3JL 1PFVA 5MLC3 3RZTA 2B63L 3S2HL 3S14L 3KYXA 1SFOL 2Y0SP 5FLML 4LHNA 2CKCA 3PL5A 4E6YA 5C4XL 3PWFA 3HKZP 3H9CA 2C6BA 3PIO1 3NFPI 3HOVL 2JI3A 3S1QL 2NVYL 3LWQB 4K9FA 4A3EL 4A3ML 1YV1A 3KYUA 3I4ML 2PYAA 1T9PA 1RDGA 4AHYA 3I4NL 4JAEA
chains in the Genus database with same CATH topology
5FJ8L 3GTKL 3S17L 5IYDL 2R93L 5C3EL 1TWCL 2E2JL 3S2DL 1I6HL 3S1ML 4A3LL 3M4OL 2NVQL 3PO2L 3M3YL 4X6AL 4A3KL 4A3CL 2JA7L 2JA8L 5IYBL 3H3VM 5IP7L 4A93L 3K7AL 2JA6L 4C2M1 3HOWL 1I3QL 3GTJL 5C44L 4BBSL 2JA5L 3CQZL 3PO3L 3FKIL 4A3IL 4Y52L 2E2HL 1TWHL 3GTOL 3HOZL 2R7ZL 1WCML 1TWAL 4A3FL 1Y1WL 4A3GL 5C4JL 1K83L 5M5WL 3RZDL 4C3JL 4BY1L 2R92L 4A3DL 4A3BL 2WAQP 3GTQL 1TWFL 4A3JL 2PMZP 2YU9L 3RZOL 5M3FL 3GTGL 3GTLL 2B63L 1TWGL 3S2HL 1Y1VL 4AYBP 3S14L 2E2IL 4BBRL 3S16L 1SFOL 2Y0SP 4QIWP 5M5YL 1R9TL 5FLML 2VUML 4BXXL 4Y7NL 5M3ML 3HOUL 5M5XL 3GTPL 3HOYL 5C4XL 3HKZP 3S15L 2NVTL 3GTML 3HOVL 3HOXL 3S1NL 2NVYL 3S1QL 5IP9L 4C3HL 2WB1P 4A3EL 4A3ML 4C3IL 3I4ML 3S1RL 3H0GL 2NVXL 5IYCL 4BY7L 1I50L 3I4NL
chains in the Genus database with same CATH homology


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