2JA8L

Cpd lesion containing rna polymerase ii elongation complex d
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 LARGEST SUBUNIT
publication title Cpd Damage Recognition by Transcribing RNA Polymerase II.
pubmed doi rcsb
molecule tags Transferase
total genus 1
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2006-11-23

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 2ja8L00
1Y1VL 4BXXL 3S14L 4C3JL 2JA5L 4A93L 4C3IL 3GTPL 4Y7NL 3GTKL 1Y1WL 4A3IL 2YU9L 3S1ML 3RZDL 5IP9L 2VUML 4QIWP 5IP7L 3CQZL 5M5YL 4BY1L 4X6AL 5C4JL 2NVTL 3M3YL 3K7AL 2WB1P 1TWFL 3HOVL 2JA7L 3S15L 2R93L 1R9TL 3RZOL 5C3EL 3HOYL 3I4NL 2WAQP 5C4XL 1K83L 5IYCL 4A3EL 3GTLL 3H0GL 5M5XL 2E2JL 5M3ML 3HOXL 4A3ML 3S2DL 2JA8L 4A3JL 4A3DL 1TWAL 4A3KL 1TWHL 3S2HL 3M4OL 1TWCL 1I6HL 4BY7L 1I3QL 5FLML 3H3VM 2NVYL 3S17L 3S16L 4A3GL 3HOUL 1I50L 4BBSL 1TWGL 4Y52L 3GTOL 3S1NL 3GTML 3HOZL 1SFOL 2B63L 3HKZP 2E2HL 4C2M1 2NVQL 5IYDL 3S1QL 2R92L 5C44L 3GTGL 4AYBP 4A3LL 3PO3L 4A3CL 3S1RL 2PMZP 2JA6L 3GTQL 1WCML 2Y0SP 3I4ML 4A3FL 4C3HL 3GTJL 2R7ZL 4A3BL 3PO2L 2NVXL 3FKIL 3HOWL 5IYBL 5FJ8L 4BBRL 5M5WL 5M3FL 2E2IL
chains in the Genus database with same CATH superfamily
1Y1VL 2JA5L 4A93L 3P8BA 1IRNA 4Y7NL 1B2JA 1PFUA 4A3IL 1OWCA 5IP9L 3B08B 1DVBA 4BY1L 4WFN1 2JA7L 2V3BB 2L0ZA 1R9TL 4AHXA 2CR8A 5C4XL 1K83L 4POGA 5GADc 3MPSA 4V196 1VCXA 2V0FA 4LHLA 3PWFA 4JAFA 2GMGA 3P2AA 5JVH1 1R0JA 5FLML 1Z92B 3H3VM 1YUXA 3HOUL 3LWVB 3IU3I 2ERJA 2M6OA 4G6BA 3GTML 4TPUA 4AI1A 2B63L 2M4YA 1RDVA 1R0IA 4C2M1 1SMUA 2R92L 3KYWA 4A3LL 2XJTA 3HJWB 2LCQA 2PMZP 2XJSA 5EIOC 1ODHA 4XGHA 1T9OA 2O5JD 1FHHA 3GTJL 5AI3A 2NVXL 5M3FL 2E2IL 1PFVA 4BXXL 4C3JL 3WWLA 5MGNA 1LKOA 5MFPA 1FHMA 5DM61 4UY81 5RXNA 3S1ML 5AN9H 2VUML 5M5YL 1T9PA 4AHYA 2WB1P 1TWFL 3HOVL 1DX8A 1IW7D 4LHNA 1RB9A 4K9FA 2A6HD 1YUZA 2XJPA 1R0FA 1IROA 3KYXA 1ZRPA 1S24A 1S30A 5M3ML 4A3ML 5AI2A 4AI3A 2RDVA 4RXNA 1BRFA 3S17L 3S16L 1I50L 3PIP1 5MLC3 2AUSB 2B5ID 3QQCE 1YK4A 1B71A 3HKZP 5MFZA 2JI3A 2M6PA 3GTGL 1IU5A 4AR6A 3S1RL 2H12A 3PKJA 2NYDA 2C6BA 3GTQL 4ZN1B 5H1Sc 2Y0SP 4A3FL 3FKIL 3HOWL 1QYBA 5IYBL 5FJ8L 3LWOB 4BBRL 5GAGc 3LWRB 1PFYA 3VPBE 1T9QA 1JYBA 3S14L 5MF6A 2CKAA 3PKIA 1R0GA 4C3IL 3GTPL 3MQKB 1RYTA 3GTKL 1Y1WL 2CKCA 4YWMA 2ZIXA 3FDJA 2XJVA 4AR5A 5IP7L 3CQZL 1OWBA 4X6AL 2EY4E 3M3YL 4TVMA 3K7AL 3KYYA 2V0EA 2R93L 1PZXA 3RZOL 4POFA 4E6YA 3ZG6A 3H9CA 3H99A 2RFKB 5IYCL 3GTLL 4B8CD 1LTLA 2HR5A 5EINC 5M5XL 3SS2A 2E2JL 3HOXL 2AQCA 3S2DL 1IU6A 4A3DL 4A3KL 3LWQB 1QQTA 5DM71 1BE7A 1WJVA 1I3QL 2JI2A 4YWLA 1BQ9A 4BBSL 3HJYB 3MSUA 3KYUA 2K2DA 2Z3QB 1TWGL 4JAEA 2MS3A 1SMWA 3S1NL 3HOZL 2J9UB 1SFOL 3JR7A 4JAGA 2NVQL 2JI1A 2AYJA 5IYDL 2QL0A 2KKDA 1NXGA 4AYBP 4AHWA 2PVEA 3HAXC 1LKMA 1P7PA 1VZHA 4GS7D 2PYAA 1WCML 3LWPB 5GAHc 3WWNB 1NXEA 3I4ML 4C3HL 4A3BL 3PO2L 5GAEc 4AR3A 5K2ME 2VL6A 2PPTA 3H97A 2APOB 1VZGA 3J7Z1 4U671 1LKPA 3PIO1 4AI0A 3PZAA 4JADA 1QCVA 2BE5D 1E8JA 1RYQA 2YU9L 3RZDL 4QIWP 2PVXA 1YK5A 5C4JL 2NVTL 3KYVA 3LPEB 3S15L 5C3EL 2A69D 3RYGA 3HOYL 3I4NL 1RWDA 1H7VA 1CADA 2A6ED 2WAQP 3H9BA 8RXNA 4A3EL 3H0GL 1RDGA 3QVDA 1BQ8A 3A44A 3J7Y1 2JA8L 4A3JL 2KN9A 1TWAL 1TWHL 3S2HL 3M4OL 1TWCL 2DSXA 1I6HL 4BY7L 1VZIA 2NVYL 2Z3RB 2XJQA 1B2OA 3NFPI 4A3GL 2XJRA 3PL5A 1YV1A 4Y52L 3GTOL 7RXNA 1SMMA 2M4VA 6RXNA 2E2HL 4AR4A 3LNLA 2PSMC 1PFWA 1C09A 1R0HA 2XJUA 3S1QL 2C6AA 5C44L 1S2ZA 3RZ6A 3B0AB 5JVG1 3PO3L 1B13A 1CAAA 4A3CL 4AI2A 2JA6L 4XXBB 4AHZA 2A68D 1F4LA 2HVYC 1NNQA 4ME3A 2R7ZL 4ZN3B 3K35A 1BFYA 5M5WL 5IY0A 3RZTA 2ERSA
chains in the Genus database with same CATH topology
1Y1VL 4BXXL 3S14L 4C3JL 2JA5L 4A93L 4C3IL 3GTPL 4Y7NL 3GTKL 1Y1WL 4A3IL 2YU9L 3S1ML 3RZDL 5IP9L 2VUML 4QIWP 5IP7L 3CQZL 5M5YL 4BY1L 4X6AL 5C4JL 2NVTL 3M3YL 3K7AL 2WB1P 1TWFL 3HOVL 2JA7L 3S15L 2R93L 1R9TL 3RZOL 5C3EL 3HOYL 3I4NL 2WAQP 5C4XL 1K83L 5IYCL 4A3EL 3GTLL 3H0GL 5M5XL 2E2JL 5M3ML 3HOXL 4A3ML 3S2DL 2JA8L 4A3JL 4A3DL 1TWAL 4A3KL 1TWHL 3S2HL 3M4OL 1TWCL 1I6HL 4BY7L 1I3QL 5FLML 3H3VM 2NVYL 3S17L 3S16L 4A3GL 3HOUL 1I50L 4BBSL 1TWGL 4Y52L 3GTOL 3S1NL 3GTML 3HOZL 1SFOL 2B63L 3HKZP 2E2HL 4C2M1 2NVQL 5IYDL 3S1QL 2R92L 5C44L 3GTGL 4AYBP 4A3LL 3PO3L 4A3CL 3S1RL 2PMZP 2JA6L 3GTQL 1WCML 2Y0SP 3I4ML 4A3FL 4C3HL 3GTJL 2R7ZL 4A3BL 3PO2L 2NVXL 3FKIL 3HOWL 5IYBL 5FJ8L 4BBRL 5M5WL 5M3FL 2E2IL
chains in the Genus database with same CATH homology


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