1Y1VD

Refined rna polymerase ii-tfiis complex
Total Genus 41
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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
41
sequence length
218
structure length
177
Chain Sequence
b'STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY'
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
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molecule keywords DNA-directed RNA polymerase II largest subunit
publication title Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.
pubmed doi rcsb
source organism Saccharomyces cerevisiae
molecule tags Transferase/transcription
total genus 41
structure length 177
sequence length 218
ec nomenclature
pdb deposition date 2004-11-19

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D PF03874 RNA_pol_Rpb4 RNA polymerase Rpb4
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.20.1250.40 Mainly Alpha Up-down Bundle Growth Hormone; Chain: A; Growth Hormone; Chain: A; 1y1vD02
4A3MD 3HOZD 3FKID 2R7ZD 5IYCD 2VUMD 4BBSD 5IYBD 3HOXD 4A3ED 3PO2D 5IP7D 4A3JD 3HOUD 2C35A 4BY1D 4BBRD 3H3VE 4A93D 4A3ID 5C4XD 5C44D 2B63D 4A3KD 4BY7D 3PO3D 5C3ED 5IP9D 1Y1WD 1Y1VD 2JA5D 3I4ND 4A3LD 3HOVD 1WCMD 4A3BD 4BXXD 5IYDD 2R92D 4A3DD 4A3CD 4A3GD 2R93D 2JA6D 3HOYD 3HOWD 3H0GD 2JA8D 5FLMD 3AYHA 3I4MD 1Y14A 2JA7D 4A3FD
chains in the Genus database with same CATH superfamily
1BCNA 3Q1SI 4EXPA 2B8ZA 4CNIC 5C44D 4NEMA 5C3ED 1HIJA 1KF9A 4IKZA 1M4AA 3OG6A 1M49A 1A22A 4LEPA 4RS1A 3HOYD 2CFPA 1ITLA 1IJZA 3S9DA 2D9QA 4YB9D 4IKVA 1SCFA 4BBRD 1V7MV 1HWGA 1HZIA 4ZW9A 5IP9D 1Y1WD 3HOVD 1V7NV 3DGCL 2Q7NB 3NCEA 4UVMA 2CFQA 3L5WI 5TS9A 3G6DA 1HULA 2V8NA 2B8YA 3G9VB 3HOZD 1BGCA 4EXNA 1EXZA 1F45B 1GA3A 4ZWBA 1M48A 1RFBA 4W6VA 2Z3QA 3BPNA 2GMFA 5L6YC 3L5XA 4PS4A 5D6KA 1Y14A 4A3FD 4NI7A 3EJJA 1EMRA 4OAAA 5IYCD 2VUMD 4O9HA 3INKC 4YQXA 2CYKA 3BPLA 1CSGA 4BY7D 1Z7CA 1AU1A 4X51A 3NCBA 1D9CA 1PV7A 4Z5RD 4WRLB 4YPGC 3D48P 1INRA 2JA8D 2HYMB 3QAZA 2L3OA 1BBNA 4OH3A 3D85C 3O7QA 3PO3D 2XQBA 3I4ND 2B8XA 3NCFA 4O6KA 1CN4C 3H0GD 1LK3A 2O27A 3QB1A 5KNHI 4DKCA 4U4VA 1LKIA 5GXBA 1AXIA 3D87A 4NI9A 5IYBD 1GNCA 2OQPA 4IKXA 3PO2D 5IP7D 3WDOA 4U4TA 1M47A 4GS7A 4YUEC 4TPHA 1ILKA 3O7PA 4QIQA 3DLQI 1RHGA 3AYHA 4ZF7A 1BUYA 1Y6KL 3QWRB 1HUWA 3IRHA 4BY1D 4TPJA 4IU9A 3DUHC 4A3KD 3HHCA 1IL6A 2JA5D 1ITIA 4IKYA 1WCMD 5D28B 5D22A 3TGXB 4LDSA 4NN7A 1PGRA 3HOWD 4J4LC 2B90A 3DI3A 3UEZE 1CD9A 3MZGA 4DKEA 4XNJA 3UF2A 4JA3A 1BP3A 4DOHA 5EQGA 5C4XD 1D9GA 2Y5YA 5EQHA 4PYPA 1CNT1 1PVHB 1M4CA 4A3CD 5EQIA 1RW5A 1ITFA 4MHLA 1VLKA 2B91A 4LRLA 4BBSD 4A3ED 2KZ1A 1JLIA 1FYHA 3H3VE 1LQSL 4A93D 3NPZA 2O26A 1PW6A 3VA2A 2Z3RA 3UX9A 4NEJA 4GBZA 5D59A 1I1RB 4ZWCA 1A7MA 4DKFA 1ALUA 5C7XA 1N1FA 4YBQA 2C35A 1M4RA 3SE4B 4I77Z 1PY2A 3B5KA 4XNIA 3HMXB 1PV6A 4APSA 1IRLA 4J05A 1EVSA 2Q14A 4TPGA 3QB7A 2XUTA 3HOXD 4A3JD 2ILKA 4IU8A 1FG9A 1ITMA 1J7VL 1QVNA 5FUCA 3LB6A 5D72A 1EKUA 5IYDD 1B5LA 4A3GD 5C65A 3OG4A 2PSMA 1Y6NL 4A3MD 3DI2A 2E9WC 1CYLA 1AX8A 3HHRA 5D70A 4U4WA 5A2NA 3BESL 4A3BD 1WU3I 3SE3B 5LQBA 4YDYI 1ETEA 5FLMD 5A2OA 1BGDA 3QT2C 3EW3A 1PW4A 1Y6ML 4NN6A 2L3YA 1F6FA 3BPOA 4A3LD 4NKQC 4A3DD 3OQ3A 4Q65A 1RCBA 3PIWA 2Q98A 2R7ZD 3LB6B 1EERA 5FHXA 1Z92A 5E4EA 3HOUD 3PIVA 5D58A 1YKBA 2B63D 1Y1VD 3N0PA 1IARA 2B8UA 2O6IA 4D2BA 3WCYI 1HWHA 1M4BA 4IKWA 2INTA 3N06A 5D71A 2B5IA 1HGUA 2LMSA 2ERJD 4GC0A 4JR9A 3UF5A 2R93D 4GBYA 4NN5A 4ZS7A 1HIKA 1BGEA 3FKID 4DKDA 2LAGA 3NCCA 4FA8E 4ZYRA 2IL6A 4A3ID 1IK0A 2H24A 4BXXD 2R92D 1NBPA 4JREA 2D48A 2JA6D 4D2DA 4GRWA 3I4MD 2JA7D 1P9MB 4D2CA
chains in the Genus database with same CATH topology
2B91A 1BGDA 3QAZA 3QT2C 4LRLA 3Q1SI 4BBSD 1BCNA 4A3ED 2L3OA 4EXPA 2B8ZA 2KZ1A 1JLIA 1BBNA 3EW3A 1FYHA 3D85C 1Y6ML 3H3VE 1LQSL 4A93D 4NN6A 2L3YA 4CNIC 3NPZA 1F6FA 5C44D 4NEMA 3PO3D 5C3ED 2O26A 2XQBA 3BPOA 4A3LD 3I4ND 1PW6A 2B8XA 4NKQC 1HIJA 1KF9A 2Z3RA 3NCFA 4O6KA 3VA2A 1CN4C 4BXXD 1M4AA 3OG6A 3UX9A 4A3DD 4NEJA 3OQ3A 1M49A 1A22A 4RS1A 3HOYD 1RCBA 3H0GD 1LK3A 1I1RB 2O27A 3QB1A 5KNHI 1ITLA 3PIWA 2Q98A 1IJZA 4DKCA 4DKFA 1LKIA 3S9DA 1A7MA 1ALUA 1AXIA 3D87A 5C7XA 2D9QA 4NI9A 2R7ZD 5IYBD 1GNCA 2OQPA 3LB6B 1EERA 5FHXA 3PO2D 1Z92A 5E4EA 5IP7D 1N1FA 3HOUD 3PIVA 1SCFA 2C35A 4BBRD 1V7MV 1M4RA 1YKBA 1HWGA 1HZIA 1M47A 3SE4B 2B63D 4I77Z 4GS7A 1Y1WD 5IP9D 1Y1VD 1PY2A 3N0PA 3HOVD 3B5KA 1IARA 4YUEC 1V7NV 1ILKA 2B8UA 2O6IA 3DGCL 3HMXB 2Q7NB 3NCEA 3WCYI 3DLQI 1IRLA 1HWHA 1RHGA 1EVSA 3AYHA 3L5WI 1BUYA 4ZF7A 1M4BA 2Q14A 3G6DA 1HULA 5TS9A 3QB7A 2B8YA 3G9VB 3HOZD 1Y6KL 3QWRB 1HUWA 1BGCA 2INTA 3HOXD 4EXNA 3IRHA 1EXZA 3N06A 1F45B 5D71A 2B5IA 4A3JD 2ILKA 4BY1D 1FG9A 1ITMA 1GA3A 1HGUA 1J7VL 1QVNA 2ERJD 2LMSA 3DUHC 5FUCA 1M48A 3LB6A 4A3KD 3HHCA 5D72A 1IL6A 2JA5D 1RFBA 1ITIA 1WCMD 1EKUA 5D28B 2Z3QA 5D22A 3BPNA 3TGXB 3UF5A 5IYDD 1B5LA 2GMFA 5L6YC 4A3GD 3L5XA 2R93D 4NN7A 1PGRA 4PS4A 3HOWD 4J4LC 4NN5A 2B90A 1Y14A 1HIKA 3OG4A 4ZS7A 1BGEA 4A3FD 2PSMA 3DI3A 4NI7A 3EJJA 3UEZE 1EMRA 1Y6NL 4A3MD 1CD9A 3FKID 3MZGA 4DKEA 4DKDA 5IYCD 2VUMD 4O9HA 2LAGA 3UF2A 3DI2A 3INKC 1BP3A 2E9WC 4YQXA 3NCCA 1CYLA 1AX8A 3HHRA 5D70A 2CYKA 4DOHA 4FA8E 2IL6A 4A3ID 3BPLA 5C4XD 1CSGA 4BY7D 1Z7CA 1D9GA 1IK0A 1AU1A 2H24A 4X51A 3NCBA 3BESL 4A3BD 1D9CA 1CNT1 1PVHB 1WU3I 4Z5RD 3SE3B 5LQBA 1M4CA 4YDYI 2R92D 1ETEA 1NBPA 4WRLB 4YPGC 4A3CD 2D48A 3D48P 2JA6D 1INRA 1RW5A 1ITFA 4MHLA 2JA8D 5FLMD 4GRWA 2HYMB 3I4MD 2JA7D 1VLKA 1P9MB
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4A3M D;  3HOZ D;  3FKI D;  2R7Z D;  5IYC D;  2VUM D;  4BBS D;  5IYB D;  3HOX D;  4A3E D;  3PO2 D;  5IP7 D;  4A3J D;  3HOU D;  2C35 A;  4BY1 D;  4BBR D;  3H3V E;  4A93 D;  4A3I D;  5C4X D;  5C44 D;  2B63 D;  4A3K D;  4BY7 D;  3PO3 D;  5C3E D;  5IP9 D;  1Y1W D;  1Y1V D;  2JA5 D;  3I4N D;  4A3L D;  3HOV D;  1WCM D;  4A3B D;  4BXX D;  5IYD D;  2R92 D;  4A3D D;  4A3C D;  4A3G D;  2R93 D;  2JA6 D;  3HOY D;  3HOW D;  3H0G D;  2JA8 D;  5FLM D;  3AYH A;  3I4M D;  1Y14 A;  2JA7 D;  4A3F D; 
#chains in the Genus database with same CATH topology
 1BCN A;  3Q1S I;  4EXP A;  2B8Z A;  4CNI C;  5C44 D;  4NEM A;  5C3E D;  1HIJ A;  1KF9 A;  4IKZ A;  1M4A A;  3OG6 A;  1M49 A;  1A22 A;  4LEP A;  4RS1 A;  3HOY D;  2CFP A;  1ITL A;  1IJZ A;  3S9D A;  2D9Q A;  4YB9 D;  4IKV A;  1SCF A;  4BBR D;  1V7M V;  1HWG A;  1HZI A;  4ZW9 A;  5IP9 D;  1Y1W D;  3HOV D;  1V7N V;  3DGC L;  2Q7N B;  3NCE A;  4UVM A;  2CFQ A;  3L5W I;  5TS9 A;  3G6D A;  1HUL A;  2V8N A;  2B8Y A;  3G9V B;  3HOZ D;  1BGC A;  4EXN A;  1EXZ A;  1F45 B;  1GA3 A;  4ZWB A;  1M48 A;  1RFB A;  4W6V A;  2Z3Q A;  3BPN A;  2GMF A;  5L6Y C;  3L5X A;  4PS4 A;  5D6K A;  1Y14 A;  4A3F D;  4NI7 A;  3EJJ A;  1EMR A;  4OAA A;  5IYC D;  2VUM D;  4O9H A;  3INK C;  4YQX A;  2CYK A;  3BPL A;  1CSG A;  4BY7 D;  1Z7C A;  1AU1 A;  4X51 A;  3NCB A;  1D9C A;  1PV7 A;  4Z5R D;  4WRL B;  4YPG C;  3D48 P;  1INR A;  2JA8 D;  2HYM B;  3QAZ A;  2L3O A;  1BBN A;  4OH3 A;  3D85 C;  3O7Q A;  3PO3 D;  2XQB A;  3I4N D;  2B8X A;  3NCF A;  4O6K A;  1CN4 C;  3H0G D;  1LK3 A;  2O27 A;  3QB1 A;  5KNH I;  4DKC A;  4U4V A;  1LKI A;  5GXB A;  1AXI A;  3D87 A;  4NI9 A;  5IYB D;  1GNC A;  2OQP A;  4IKX A;  3PO2 D;  5IP7 D;  3WDO A;  4U4T A;  1M47 A;  4GS7 A;  4YUE C;  4TPH A;  1ILK A;  3O7P A;  4QIQ A;  3DLQ I;  1RHG A;  3AYH A;  4ZF7 A;  1BUY A;  1Y6K L;  3QWR B;  1HUW A;  3IRH A;  4BY1 D;  4TPJ A;  4IU9 A;  3DUH C;  4A3K D;  3HHC A;  1IL6 A;  2JA5 D;  1ITI A;  4IKY A;  1WCM D;  5D28 B;  5D22 A;  3TGX B;  4LDS A;  4NN7 A;  1PGR A;  3HOW D;  4J4L C;  2B90 A;  3DI3 A;  3UEZ E;  1CD9 A;  3MZG A;  4DKE A;  4XNJ A;  3UF2 A;  4JA3 A;  1BP3 A;  4DOH A;  5EQG A;  5C4X D;  1D9G A;  2Y5Y A;  5EQH A;  4PYP A;  1CNT 1;  1PVH B;  1M4C A;  4A3C D;  5EQI A;  1RW5 A;  1ITF A;  4MHL A;  1VLK A;  2B91 A;  4LRL A;  4BBS D;  4A3E D;  2KZ1 A;  1JLI A;  1FYH A;  3H3V E;  1LQS L;  4A93 D;  3NPZ A;  2O26 A;  1PW6 A;  3VA2 A;  2Z3R A;  3UX9 A;  4NEJ A;  4GBZ A;  5D59 A;  1I1R B;  4ZWC A;  1A7M A;  4DKF A;  1ALU A;  5C7X A;  1N1F A;  4YBQ A;  2C35 A;  1M4R A;  3SE4 B;  4I77 Z;  1PY2 A;  3B5K A;  4XNI A;  3HMX B;  1PV6 A;  4APS A;  1IRL A;  4J05 A;  1EVS A;  2Q14 A;  4TPG A;  3QB7 A;  2XUT A;  3HOX D;  4A3J D;  2ILK A;  4IU8 A;  1FG9 A;  1ITM A;  1J7V L;  1QVN A;  5FUC A;  3LB6 A;  5D72 A;  1EKU A;  5IYD D;  1B5L A;  4A3G D;  5C65 A;  3OG4 A;  2PSM A;  1Y6N L;  4A3M D;  3DI2 A;  2E9W C;  1CYL A;  1AX8 A;  3HHR A;  5D70 A;  4U4W A;  5A2N A;  3BES L;  4A3B D;  1WU3 I;  3SE3 B;  5LQB A;  4YDY I;  1ETE A;  5FLM D;  5A2O A;  1BGD A;  3QT2 C;  3EW3 A;  1PW4 A;  1Y6M L;  4NN6 A;  2L3Y A;  1F6F A;  3BPO A;  4A3L D;  4NKQ C;  4A3D D;  3OQ3 A;  4Q65 A;  1RCB A;  3PIW A;  2Q98 A;  2R7Z D;  3LB6 B;  1EER A;  5FHX A;  1Z92 A;  5E4E A;  3HOU D;  3PIV A;  5D58 A;  1YKB A;  2B63 D;  1Y1V D;  3N0P A;  1IAR A;  2B8U A;  2O6I A;  4D2B A;  3WCY I;  1HWH A;  1M4B A;  4IKW A;  2INT A;  3N06 A;  5D71 A;  2B5I A;  1HGU A;  2LMS A;  2ERJ D;  4GC0 A;  4JR9 A;  3UF5 A;  2R93 D;  4GBY A;  4NN5 A;  4ZS7 A;  1HIK A;  1BGE A;  3FKI D;  4DKD A;  2LAG A;  3NCC A;  4FA8 E;  4ZYR A;  2IL6 A;  4A3I D;  1IK0 A;  2H24 A;  4BXX D;  2R92 D;  1NBP A;  4JRE A;  2D48 A;  2JA6 D;  4D2D A;  4GRW A;  3I4M D;  2JA7 D;  1P9M B;  4D2C A; 
#chains in the Genus database with same CATH homology
 2B91 A;  1BGD A;  3QAZ A;  3QT2 C;  4LRL A;  3Q1S I;  4BBS D;  1BCN A;  4A3E D;  2L3O A;  4EXP A;  2B8Z A;  2KZ1 A;  1JLI A;  1BBN A;  3EW3 A;  1FYH A;  3D85 C;  1Y6M L;  3H3V E;  1LQS L;  4A93 D;  4NN6 A;  2L3Y A;  4CNI C;  3NPZ A;  1F6F A;  5C44 D;  4NEM A;  3PO3 D;  5C3E D;  2O26 A;  2XQB A;  3BPO A;  4A3L D;  3I4N D;  1PW6 A;  2B8X A;  4NKQ C;  1HIJ A;  1KF9 A;  2Z3R A;  3NCF A;  4O6K A;  3VA2 A;  1CN4 C;  4BXX D;  1M4A A;  3OG6 A;  3UX9 A;  4A3D D;  4NEJ A;  3OQ3 A;  1M49 A;  1A22 A;  4RS1 A;  3HOY D;  1RCB A;  3H0G D;  1LK3 A;  1I1R B;  2O27 A;  3QB1 A;  5KNH I;  1ITL A;  3PIW A;  2Q98 A;  1IJZ A;  4DKC A;  4DKF A;  1LKI A;  3S9D A;  1A7M A;  1ALU A;  1AXI A;  3D87 A;  5C7X A;  2D9Q A;  4NI9 A;  2R7Z D;  5IYB D;  1GNC A;  2OQP A;  3LB6 B;  1EER A;  5FHX A;  3PO2 D;  1Z92 A;  5E4E A;  5IP7 D;  1N1F A;  3HOU D;  3PIV A;  1SCF A;  2C35 A;  4BBR D;  1V7M V;  1M4R A;  1YKB A;  1HWG A;  1HZI A;  1M47 A;  3SE4 B;  2B63 D;  4I77 Z;  4GS7 A;  1Y1W D;  5IP9 D;  1Y1V D;  1PY2 A;  3N0P A;  3HOV D;  3B5K A;  1IAR A;  4YUE C;  1V7N V;  1ILK A;  2B8U A;  2O6I A;  3DGC L;  3HMX B;  2Q7N B;  3NCE A;  3WCY I;  3DLQ I;  1IRL A;  1HWH A;  1RHG A;  1EVS A;  3AYH A;  3L5W I;  1BUY A;  4ZF7 A;  1M4B A;  2Q14 A;  3G6D A;  1HUL A;  5TS9 A;  3QB7 A;  2B8Y A;  3G9V B;  3HOZ D;  1Y6K L;  3QWR B;  1HUW A;  1BGC A;  2INT A;  3HOX D;  4EXN A;  3IRH A;  1EXZ A;  3N06 A;  1F45 B;  5D71 A;  2B5I A;  4A3J D;  2ILK A;  4BY1 D;  1FG9 A;  1ITM A;  1GA3 A;  1HGU A;  1J7V L;  1QVN A;  2ERJ D;  2LMS A;  3DUH C;  5FUC A;  1M48 A;  3LB6 A;  4A3K D;  3HHC A;  5D72 A;  1IL6 A;  2JA5 D;  1RFB A;  1ITI A;  1WCM D;  1EKU A;  5D28 B;  2Z3Q A;  5D22 A;  3BPN A;  3TGX B;  3UF5 A;  5IYD D;  1B5L A;  2GMF A;  5L6Y C;  4A3G D;  3L5X A;  2R93 D;  4NN7 A;  1PGR A;  4PS4 A;  3HOW D;  4J4L C;  4NN5 A;  2B90 A;  1Y14 A;  1HIK A;  3OG4 A;  4ZS7 A;  1BGE A;  4A3F D;  2PSM A;  3DI3 A;  4NI7 A;  3EJJ A;  3UEZ E;  1EMR A;  1Y6N L;  4A3M D;  1CD9 A;  3FKI D;  3MZG A;  4DKE A;  4DKD A;  5IYC D;  2VUM D;  4O9H A;  2LAG A;  3UF2 A;  3DI2 A;  3INK C;  1BP3 A;  2E9W C;  4YQX A;  3NCC A;  1CYL A;  1AX8 A;  3HHR A;  5D70 A;  2CYK A;  4DOH A;  4FA8 E;  2IL6 A;  4A3I D;  3BPL A;  5C4X D;  1CSG A;  4BY7 D;  1Z7C A;  1D9G A;  1IK0 A;  1AU1 A;  2H24 A;  4X51 A;  3NCB A;  3BES L;  4A3B D;  1D9C A;  1CNT 1;  1PVH B;  1WU3 I;  4Z5R D;  3SE3 B;  5LQB A;  1M4C A;  4YDY I;  2R92 D;  1ETE A;  1NBP A;  4WRL B;  4YPG C;  4A3C D;  2D48 A;  3D48 P;  2JA6 D;  1INR A;  1RW5 A;  1ITF A;  4MHL A;  2JA8 D;  5FLM D;  4GRW A;  2HYM B;  3I4M D;  2JA7 D;  1VLK A;  1P9M B; 
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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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