4X6AL

Crystal structure of yeast rna polymerase ii encountering oxidative cyclopurine dna lesions
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 subunit RPB1
publication title Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions.
pubmed doi rcsb
molecule tags Transcription/dna
total genus 1
structure length 46
sequence length 46
ec nomenclature
pdb deposition date 2014-12-07

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 4x6aL00
4A3LL 4A3JL 2B63L 3GTGL 3GTPL 4C3JL 3M3YL 2JA8L 1TWCL 1I50L 4Y7NL 4A3BL 2PMZP 2R7ZL 4C3HL 2R92L 4C2M1 3CQZL 3K7AL 5IYCL 4A3DL 4Y52L 1I6HL 5M5XL 3HOZL 3S1ML 1TWFL 3I4ML 2E2JL 3PO3L 2VUML 2JA7L 2YU9L 3H3VM 1K83L 3RZOL 3GTQL 3I4NL 3S16L 4A3GL 3GTLL 3FKIL 5C44L 5IYBL 2NVTL 5C3EL 5C4XL 3S17L 3GTOL 4X6AL 4BY7L 4BBRL 3S14L 2R93L 2JA6L 5FJ8L 5IYDL 3S2HL 4A3CL 4A3KL 3M4OL 1R9TL 4A93L 3HOUL 3H0GL 2NVXL 5IP9L 1TWAL 2JA5L 4C3IL 3S1NL 3GTKL 4AYBP 3S1RL 3RZDL 5M5YL 4BXXL 4QIWP 3HOYL 3GTJL 2NVQL 3S2DL 4A3EL 2WAQP 5FLML 3GTML 3HOVL 5IP7L 2NVYL 2E2IL 3HKZP 4BY1L 5C4JL 2Y0SP 2WB1P 1Y1WL 1I3QL 1TWHL 1TWGL 3S1QL 3HOXL 3S15L 4A3IL 1Y1VL 4A3ML 5M3FL 4BBSL 1SFOL 1WCML 5M3ML 2E2HL 5M5WL 4A3FL 3HOWL 3PO2L
chains in the Genus database with same CATH superfamily
1CADA 5K2ME 1IROA 3GTPL 4LHLA 2BE5D 3K35A 3LWRB 2JA8L 2B5ID 1LKOA 1S30A 3MQKB 5DM71 4Y7NL 1R0HA 2R7ZL 4C3HL 1Z92B 1T9QA 1YUXA 4JAGA 2PVEA 1BE7A 3I4ML 2E2JL 3PO3L 3P8BA 2VUML 4UY81 1K83L 4JAEA 4V196 4AI1A 5AI3A 4B8CD 2C6AA 5IYBL 1FHHA 5C3EL 3S17L 4AI0A 4RXNA 1WJVA 3GTOL 1NXEA 2PSMC 4AR4A 4BBRL 2Z3QB 1BRFA 5IYDL 5FJ8L 1QCVA 1QYBA 4A3KL 3NFPI 1R0JA 1R9TL 4A93L 7RXNA 2C6BA 2NVXL 3MPSA 3MSUA 2ERSA 2M4YA 3WWNB 1OWCA 3KYYA 2WAQP 2JI2A 2V0FA 3GTML 2NVYL 2PVXA 2AUSB 4GS7D 3H9BA 2JI1A 4AHXA 1I3QL 1TWGL 3J7Y1 2L0ZA 3P2AA 3IU3I 1NXGA 2CR8A 5AN9H 2E2HL 3PWFA 3HOWL 3RYGA 4A3JL 3GTGL 5IY0A 2HR5A 3SS2A 4AHZA 1BFYA 2GMGA 1RB9A 1YK5A 4C2M1 1R0GA 1S2ZA 5GAHc 1RYTA 5IYCL 5M5XL 3S1ML 1BQ8A 1B71A 1YK4A 4YWLA 3GTQL 3S16L 1R0FA 3GTLL 3FKIL 4WFN1 5C4XL 4X6AL 3S14L 4POFA 4A3CL 4AHWA 3B08B 3HOUL 4XXBB 5AI2A 2VL6A 6RXNA 4C3IL 1PZXA 3S1NL 3S1RL 2XJTA 5MFPA 5M5YL 5MFZA 3PIO1 2LCQA 4A3EL 5GAGc 1B2OA 1C09A 3HOVL 1P7PA 1IU5A 5IP7L 1SMUA 2E2IL 3HKZP 3KYVA 1RDGA 2XJQA 5C4JL 1S24A 2WB1P 1BQ9A 1TWHL 3S1QL 1E8JA 3S15L 1FHMA 1R0IA 4A3ML 1NNQA 2JI3A 4BBSL 4U671 1YV1A 4A3LL 2Z3RB 1CAAA 1QQTA 3PKIA 4C3JL 2J9UB 2ERJA 3LWPB 3LWVB 4TPUA 4A3BL 3QQCE 2A6HD 2PMZP 4AR6A 2R92L 4POGA 5JVG1 1RWDA 4Y52L 1I6HL 5GADc 3HJYB 4AI3A 1SMMA 2V3BB 2JA7L 1IW7D 5DM61 3H3VM 2V0EA 3RZOL 3KYWA 2CKAA 2NVTL 4BY7L 4AHYA 1VZIA 5JVH1 1RYQA 3S2HL 3RZ6A 2XJPA 2DSXA 3M4OL 3H0GL 2A68D 2ZIXA 4ME3A 1ODHA 2M6OA 3PKJA 1TWAL 3VPBE 2JA5L 2KN9A 2XJUA 3GTKL 4AYBP 1IU6A 1PFWA 3H99A 2NVQL 2APOB 3PL5A 1VZHA 3WWLA 1IRNA 1PFUA 5FLML 1H7VA 2HVYC 2XJRA 2Y0SP 4YWMA 4E6YA 1Y1WL 1LTLA 2H12A 2CKCA 3HOXL 4JAFA 2PYAA 2A6ED 1PFVA 1F4LA 1SFOL 1T9PA 5M5WL 1RDVA 3PO2L 3H9CA 1SMWA 2B63L 1PFYA 4G6BA 3M3YL 5MLC3 1TWCL 2M6PA 1I50L 2EY4E 3RZTA 1DX8A 2K2DA 3KYXA 3CQZL 3K7AL 3A44A 4A3DL 3LPEB 3HOZL 1TWFL 3HAXC 4TVMA 4AR5A 5EINC 2M4VA 2YU9L 4AR3A 3I4NL 4A3GL 1VCXA 5C44L 2KKDA 2O5JD 4ZN3B 3B0AB 5RXNA 3QVDA 2PPTA 2RDVA 1T9OA 5MF6A 2XJVA 1B13A 4ZN1B 3PIP1 2R93L 4JADA 2JA6L 1LKMA 1B2JA 3LNLA 3HJWB 5IP9L 1ZRPA 1JYBA 2A69D 4LHNA 2AQCA 1LKPA 2NYDA 3RZDL 3LWQB 2MS3A 4BXXL 4QIWP 3HOYL 3GTJL 2QL0A 3S2DL 3KYUA 3JR7A 1YUZA 5EIOC 8RXNA 1DVBA 3J7Z1 2AYJA 3H97A 1OWBA 4XGHA 3LWOB 4BY1L 3PZAA 5H1Sc 2RFKB 3ZG6A 4A3IL 1VZGA 1Y1VL 5MGNA 5M3FL 2XJSA 1WCML 5M3ML 4A3FL 3FDJA 5GAEc 4AI2A 4K9FA
chains in the Genus database with same CATH topology
4A3LL 4A3JL 2B63L 3GTGL 3GTPL 4C3JL 3M3YL 2JA8L 1TWCL 1I50L 4Y7NL 4A3BL 2PMZP 2R7ZL 4C3HL 2R92L 4C2M1 3CQZL 3K7AL 5IYCL 4A3DL 4Y52L 1I6HL 5M5XL 3HOZL 3S1ML 1TWFL 3I4ML 2E2JL 3PO3L 2VUML 2JA7L 2YU9L 3H3VM 1K83L 3RZOL 3GTQL 3I4NL 3S16L 4A3GL 3GTLL 3FKIL 5C44L 5IYBL 2NVTL 5C3EL 5C4XL 3S17L 3GTOL 4X6AL 4BY7L 4BBRL 3S14L 2R93L 2JA6L 5FJ8L 5IYDL 3S2HL 4A3CL 4A3KL 3M4OL 1R9TL 4A93L 3HOUL 3H0GL 2NVXL 5IP9L 1TWAL 2JA5L 4C3IL 3S1NL 3GTKL 4AYBP 3S1RL 3RZDL 5M5YL 4BXXL 4QIWP 3HOYL 3GTJL 2NVQL 3S2DL 4A3EL 2WAQP 5FLML 3GTML 3HOVL 5IP7L 2NVYL 2E2IL 3HKZP 4BY1L 5C4JL 2Y0SP 2WB1P 1Y1WL 1I3QL 1TWHL 1TWGL 3S1QL 3HOXL 3S15L 4A3IL 1Y1VL 4A3ML 5M3FL 4BBSL 1SFOL 1WCML 5M3ML 2E2HL 5M5WL 4A3FL 3HOWL 3PO2L
chains in the Genus database with same CATH homology


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