4BBRL

Structure of rna polymerase ii-tfiib complex
Total Genus 4
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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
4
sequence length
44
structure length
44
Chain Sequence
LKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR
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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 Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex
pubmed doi rcsb
source organism Saccharomyces cerevisiae
molecule tags Transcription
total genus 4
structure length 44
sequence length 44
ec nomenclature
pdb deposition date 2012-09-27

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 4bbrL00
3FKIL 5M3ML 3M4OL 3S17L 2VUML 3S16L 3PO2L 3S2HL 5C44L 5IP7L 2B63L 3S14L 4C3IL 3HOXL 4Y52L 3HKZP 4C3HL 4A3EL 1TWCL 3HOYL 3GTJL 5IYCL 1Y1WL 3RZOL 4Y7NL 1TWGL 3S1ML 1TWHL 1TWAL 3GTML 3S1NL 3HOVL 2PMZP 4BXXL 4A3GL 2JA5L 5M5XL 3S1QL 4BY7L 3M3YL 1SFOL 4A3FL 1TWFL 3H0GL 2NVTL 5M5YL 1R9TL 2E2JL 3RZDL 2WB1P 3GTGL 3CQZL 3S15L 4A93L 2E2HL 5C4JL 5FJ8L 3K7AL 3GTLL 4QIWP 4A3KL 4BY1L 2R92L 2R93L 4BBSL 4A3IL 2R7ZL 5IYBL 5IYDL 1WCML 3S2DL 2YU9L 3GTOL 3GTQL 3PO3L 2NVYL 5M5WL 2JA7L 5IP9L 4BBRL 1I6HL 5C3EL 3HOWL 3I4NL 5C4XL 4A3CL 4C3JL 4A3DL 2WAQP 3HOUL 4A3JL 5M3FL 3S1RL 1I50L 5FLML 3GTPL 2NVXL 4A3BL 3HOZL 2E2IL 1K83L 2NVQL 4AYBP 1I3QL 1Y1VL 4X6AL 4C2M1 4A3ML 3H3VM 2JA8L 3I4ML 4A3LL 2JA6L 2Y0SP 3GTKL
chains in the Genus database with same CATH superfamily
3S17L 5EIOC 3S16L 4XXBB 4ZN1B 3S2HL 1IU5A 2XJSA 5C44L 1YK5A 3HOXL 3H9CA 1R0HA 4POFA 1TWCL 3GTJL 4TVMA 3LWQB 3S1ML 2MS3A 4AHZA 4AHWA 2ZIXA 3GTML 3KYVA 3HOVL 5JVH1 5M5XL 4BY7L 3M3YL 1SFOL 1T9OA 2A68D 2C6AA 1PFUA 2PYAA 2BE5D 5M5YL 2CKAA 4AI2A 3S15L 1OWCA 2HVYC 2PSMC 1NXEA 4QIWP 2R92L 1PZXA 4BBSL 1BE7A 3KYUA 4A3IL 4AI0A 2LCQA 3WWLA 2K2DA 2EY4E 3S2DL 3GTQL 3LWRB 4AR3A 1IROA 5M5WL 4LHNA 4UY81 2M4VA 3PWFA 3NFPI 3I4NL 4A3CL 2A69D 2CR8A 3HOUL 1I50L 5FLML 1VZHA 3GTPL 3PKJA 1ODHA 3HOZL 1LKPA 1S30A 2NVQL 1Y1VL 1BRFA 2H12A 5MLC3 2JA8L 3I4ML 4A3LL 2M4YA 3FKIL 3MPSA 5M3ML 5GAEc 1R0IA 2VUML 3LNLA 1WJVA 3MQKB 1CADA 1VZGA 3FDJA 1F4LA 4RXNA 1OWBA 3HOYL 4GS7D 2Z3QB 3J7Y1 1SMUA 1Y1WL 1IRNA 1RDVA 5GADc 4AHXA 3S1NL 1CAAA 2L0ZA 3A44A 5MFPA 4A3GL 5IY0A 1YUZA 1B71A 3WWNB 1QQTA 1PFWA 2M6OA 2NVTL 1T9PA 2V0EA 2XJUA 5AN9H 4JAGA 3CQZL 2E2HL 5FJ8L 1BQ9A 4JAFA 1YV1A 2A6HD 4A3KL 4BY1L 1P7PA 2R93L 2B5ID 2R7ZL 3SS2A 5GAGc 1WCML 3RZTA 2YU9L 1BFYA 2JI3A 2NVYL 3IU3I 3KYWA 2AQCA 4ME3A 3RZ6A 4G6BA 4AR5A 3VPBE 3J7Z1 1LTLA 3LPEB 3S1RL 4K9FA 4V196 5H1Sc 3B08B 1RYQA 1VCXA 1LKMA 2O5JD 1I3QL 1DX8A 3H97A 4A3ML 5GAHc 2NYDA 4AHYA 3M4OL 1Z92B 2PVEA 1ZRPA 2VL6A 1B13A 3PO2L 1SMWA 3S14L 3LWVB 3JR7A 2Z3RB 2RDVA 1C09A 5IYCL 4AR6A 5MGNA 3PIP1 1TWGL 1TWHL 1PFYA 2QL0A 1TWAL 3LWPB 2PVXA 8RXNA 2PPTA 2PMZP 4TPUA 4BXXL 4AR4A 3S1QL 3HAXC 4A3FL 1R0GA 2J9UB 3HJWB 4JAEA 2XJRA 3H0GL 5AI2A 1R9TL 3RZDL 2WB1P 5C4JL 4B8CD 2XJVA 3KYYA 5RXNA 1QCVA 5IYBL 2CKCA 5DM61 5DM71 2A6ED 5IYDL 2XJPA 1IW7D 3PO3L 4POGA 1NXGA 2JA7L 1VZIA 3P8BA 4BBRL 2AUSB 1PFVA 5C3EL 1BQ8A 1RWDA 4A3DL 3PL5A 4A3JL 5M3FL 3ZG6A 4WFN1 1NNQA 5K2ME 2C6BA 3H99A 2NVXL 3PZAA 1DVBA 1R0JA 4AYBP 3QVDA 1S24A 1B2JA 2APOB 1RB9A 4C2M1 3H3VM 4JADA 2JA6L 1B2OA 2Y0SP 2V3BB 3GTKL 2GMGA 1FHMA 5MF6A 1RDGA 5IP7L 2B63L 2RFKB 4C3IL 3PKIA 4Y52L 3HKZP 3RYGA 4C3HL 2DSXA 4A3EL 4YWMA 6RXNA 3RZOL 4Y7NL 5JVG1 3MSUA 3KYXA 5EINC 2KKDA 2JA5L 1R0FA 4E6YA 1TWFL 2KN9A 1YUXA 1S2ZA 1LKOA 2ERSA 3B0AB 3P2AA 3K35A 4ZN3B 3LWOB 2E2JL 3GTGL 4A93L 4LHLA 3K7AL 3GTLL 4AI3A 4YWLA 1E8JA 2JI1A 4XGHA 1H7VA 3QQCE 2XJTA 3PIO1 4U671 2JI2A 4AI1A 2M6PA 2V0FA 3GTOL 5MFZA 5IP9L 1YK4A 7RXNA 1I6HL 5AI3A 3HOWL 5C4XL 4C3JL 2ERJA 2WAQP 1QYBA 1JYBA 1IU6A 4A3BL 1FHHA 1SMMA 2XJQA 3H9BA 2E2IL 1K83L 1RYTA 1T9QA 4X6AL 3HJYB 2HR5A 2AYJA
chains in the Genus database with same CATH topology
3FKIL 5M3ML 3M4OL 3S17L 2VUML 3S16L 3PO2L 3S2HL 5C44L 5IP7L 2B63L 3S14L 4C3IL 3HOXL 4Y52L 3HKZP 4C3HL 4A3EL 1TWCL 3HOYL 3GTJL 5IYCL 1Y1WL 3RZOL 4Y7NL 1TWGL 3S1ML 1TWHL 1TWAL 3GTML 3S1NL 3HOVL 2PMZP 4BXXL 4A3GL 2JA5L 5M5XL 3S1QL 4BY7L 3M3YL 1SFOL 4A3FL 1TWFL 3H0GL 2NVTL 5M5YL 1R9TL 2E2JL 3RZDL 2WB1P 3GTGL 3CQZL 3S15L 4A93L 2E2HL 5C4JL 5FJ8L 3K7AL 3GTLL 4QIWP 4A3KL 4BY1L 2R92L 2R93L 4BBSL 4A3IL 2R7ZL 5IYBL 5IYDL 1WCML 3S2DL 2YU9L 3GTOL 3GTQL 3PO3L 2NVYL 5M5WL 2JA7L 5IP9L 4BBRL 1I6HL 5C3EL 3HOWL 3I4NL 5C4XL 4A3CL 4C3JL 4A3DL 2WAQP 3HOUL 4A3JL 5M3FL 3S1RL 1I50L 5FLML 3GTPL 2NVXL 4A3BL 3HOZL 2E2IL 1K83L 2NVQL 4AYBP 1I3QL 1Y1VL 4X6AL 4C2M1 4A3ML 3H3VM 2JA8L 3I4ML 4A3LL 2JA6L 2Y0SP 3GTKL
chains in the Genus database with same CATH homology


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