3HOYD

Complete rna polymerase ii elongation complex vi
Total Genus 49
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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
49
sequence length
218
structure length
178
Chain Sequence
STSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY
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 tags Transcription,transferase/dna/rna hybrid
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
pubmed doi rcsb
total genus 49
structure length 178
sequence length 218
ec nomenclature
pdb deposition date 2009-06-03

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; 3hoyD02
4A3ID 3I4ND 2B63D 4A3BD 5IP9D 2R92D 4BY1D 3PO2D 2VUMD 3H3VE 1Y14A 5IYDD 5C4XD 2JA7D 3PO3D 2JA6D 3AYHA 4A3JD 1Y1VD 2R7ZD 4A93D 2R93D 2C35A 4BBRD 1Y1WD 3HOWD 4A3CD 5C3ED 4A3ED 4A3MD 5C44D 3HOYD 4A3KD 5IP7D 3HOUD 3I4MD 3HOXD 4BBSD 4A3GD 1WCMD 3HOVD 2JA5D 4A3FD 4BXXD 5FLMD 4A3LD 2JA8D 3FKID 5IYCD 3H0GD 4BY7D 5IYBD 3HOZD 4A3DD
chains in the Genus database with same CATH superfamily
3B5KA 3MZGA 2D9QA 5L6YC 3D87A 3DLQI 4PYPA 2JA7D 1YKBA 1GA3A 4U4TA 4A93D 4YQXA 5D71A 3NCFA 4U4VA 1IRLA 1KF9A 4Z5RD 3G9VB 2B8XA 1PY2A 1WCMD 1ETEA 1HIJA 4ZW9A 2O6IA 1Z7CA 3FKID 5FHXA 3UX9A 1FG9A 4YPGC 5LQBA 2CFPA 1HIKA 4D2DA 2R93D 1CSGA 1F6FA 4NI9A 1HULA 4JR9A 3UF2A 5A2OA 2JA5D 3NPZA 1LQSL 1V7NV 1JLIA 4BY7D 2B63D 3INKC 4IU8A 3OQ3A 1PGRA 5KNHI 1M4RA 4BBRD 2IL6A 3SE4B 3UF5A 1PW6A 2KZ1A 1HWGA 5D59A 1BGEA 3OG6A 3NCBA 4IKZA 5D58A 4A3LD 1BP3A 3VA2A 5C4XD 3DI3A 2R92D 1IJZA 4CNIC 3HOWD 1BCNA 5GXBA 1BGCA 4DKEA 3HOUD 1HWHA 5D6KA 4ZYRA 1ITIA 3PO3D 4NN5A 1BGDA 1EMRA 2D48A 2B90A 4ZWBA 1A7MA 2R7ZD 4DKCA 1IL6A 1HZIA 4A3ED 2PSMA 3EJJA 4GBYA 5EQIA 5IYCD 3NCEA 4Q65A 1LK3A 3UEZE 4LRLA 5EQGA 1VLKA 4GRWA 1BUYA 4RS1A 1HUWA 3LB6B 2O26A 4IKVA 3NCCA 5D72A 2B8ZA 1RHGA 1Y6ML 1A22A 1M4AA 5EQHA 2L3YA 1B5LA 3HOZD 4YDYI 4O9HA 3L5XA 4EXPA 2CYKA 2C35A 5D70A 4U4WA 4EXNA 3BPOA 1ITMA 5IP7D 4NN7A 1LKIA 2O27A 4ZS7A 3H0GD 3D85C 3HMXB 1QVNA 3PO2D 4XNIA 2B8YA 2Z3QA 1M4BA 1Y1VD 1RCBA 1Y1WD 4W6VA 4MHLA 5D22A 2Q14A 1RW5A 3DUHC 4NEMA 3IRHA 4FA8E 2Z3RA 1ALUA 1Y6KL 2Y5YA 4TPJA 4I77Z 1N1FA 3O7QA 1SCFA 4J05A 4LDSA 3QB7A 2Q98A 2H24A 2CFQA 3O7PA 4OH3A 1EERA 4NN6A 3OG4A 4IKWA 2ILKA 3HHRA 3N06A 2JA8D 2XUTA 4WRLB 4A3DD 3I4ND 3DGCL 5E4EA 2ERJD 4NKQC 1F45B 4DOHA 3DI2A 3D48P 4A3MD 3HOYD 1PV7A 4ZF7A 4BBSD 4LEPA 3SE3B 1BBNA 1AU1A 3WCYI 5D28B 4XNJA 4BY1D 4J4LC 1J7VL 2VUMD 4QIQA 3QAZA 1HGUA 4YUEC 4YBQA 4A3JD 3PIWA 1Z92A 3EW3A 2LMSA 3I4MD 2Q7NB 4A3FD 4JREA 3S9DA 5FLMD 3BPLA 1RFBA 3G6DA 2L3OA 1FYHA 1M4CA 1EKUA 2INTA 1V7MV 4TPGA 4IKYA 2LAGA 4A3KD 3LB6A 3HOXD 1CD9A 3WDOA 1P9MB 3BPNA 4YB9D 4A3BD 5A2NA 3H3VE 2B8UA 4GBZA 2GMFA 2JA6D 1WU3I 3QWRB 4NEJA 1IK0A 5C3ED 2E9WC 1I1RB 4ZWCA 4IKXA 1M49A 4NI7A 5IP9D 1M47A 1Y6NL 2HYMB 3Q1SI 3N0PA 3TGXB 3PIVA 1GNCA 5FUCA 4X51A 3QT2C 1EXZA 2B5IA 1CNT1 1AXIA 4JA3A 4DKFA 4DKDA 1INRA 5C7XA 1AX8A 4TPHA 3QB1A 1Y14A 5C65A 4PS4A 4A3CD 5TS9A 1CN4C 4D2CA 5C44D 1EVSA 1D9GA 4O6KA 4D2BA 1D9CA 1PV6A 4BXXD 2OQPA 1ILKA 5IYBD 4A3ID 1NBPA 3L5WI 3BESL 4OAAA 1IARA 5IYDD 2XQBA 3AYHA 2V8NA 1M48A 4IU9A 4GC0A 1PW4A 2B91A 4APSA 4A3GD 4GS7A 3HOVD 1CYLA 1ITLA 4UVMA 1PVHB 3HHCA 1ITFA
chains in the Genus database with same CATH topology
4I77Z 1EMRA 4A3BD 1N1FA 3B5KA 3MZGA 1SCFA 2D48A 2D9QA 5L6YC 3D87A 3H3VE 2B8UA 3DLQI 3QB7A 2B90A 2JA7D 2Q98A 2GMFA 1YKBA 2JA6D 1WU3I 2H24A 3QWRB 1GA3A 1A7MA 2R7ZD 4NEJA 4YQXA 4A93D 4DKCA 1IK0A 5D71A 5C3ED 2E9WC 1IL6A 3NCFA 1HZIA 4A3ED 1I1RB 1IRLA 1KF9A 1EERA 4NN6A 4Z5RD 3G9VB 3OG4A 2B8XA 1PY2A 1WCMD 1ETEA 2PSMA 1HIJA 2ILKA 3HHRA 3EJJA 1M49A 4NI7A 2O6IA 1Z7CA 3N06A 3FKID 5IYCD 2JA8D 3NCEA 4WRLB 4A3DD 5FHXA 1LK3A 3I4ND 3UX9A 1FG9A 4YPGC 5IP9D 3UEZE 1M47A 3DGCL 4LRLA 5E4EA 2ERJD 5LQBA 4NKQC 1F45B 4DOHA 1VLKA 1Y6NL 2HYMB 3Q1SI 3N0PA 4GRWA 1BUYA 3TGXB 1HIKA 4RS1A 3PIVA 1GNCA 2R93D 5FUCA 1HUWA 3DI2A 4X51A 3D48P 2O26A 3LB6B 1CSGA 3QT2C 4A3MD 3NCCA 1F6FA 5D72A 3HOYD 1EXZA 2B5IA 2B8ZA 4NI9A 4ZF7A 1RHGA 1HULA 4BBSD 1CNT1 1Y6ML 1A22A 1AXIA 3UF2A 2JA5D 1M4AA 3NPZA 3SE3B 2L3YA 1LQSL 1V7NV 1JLIA 1BBNA 1B5LA 4BY7D 3HOZD 1AU1A 4DKFA 4DKDA 4YDYI 3WCYI 2B63D 1INRA 5C7XA 5D28B 1AX8A 4O9HA 4BY1D 4J4LC 3INKC 1J7VL 2VUMD 3QAZA 3QB1A 1Y14A 1HGUA 3OQ3A 3L5XA 4EXPA 1PGRA 4YUEC 4PS4A 2CYKA 5KNHI 4A3JD 3PIWA 1M4RA 1Z92A 2C35A 5D70A 4BBRD 4EXNA 5TS9A 4A3CD 2IL6A 3SE4B 1CN4C 1PW6A 3UF5A 2KZ1A 3EW3A 5C44D 1EVSA 3BPOA 1ITMA 1HWGA 5IP7D 1D9GA 2LMSA 3I4MD 4O6KA 1BGEA 1D9CA 2Q7NB 4NN7A 3OG6A 4A3FD 4BXXD 1LKIA 3NCBA 3BPLA 2OQPA 3S9DA 2O27A 5FLMD 4A3LD 1BP3A 3VA2A 1RFBA 3G6DA 1ILKA 3DI3A 2L3OA 3H0GD 4ZS7A 5IYBD 1FYHA 5C4XD 4A3ID 1M4CA 2R92D 3D85C 3HMXB 1QVNA 1NBPA 3L5WI 3PO2D 3BESL 1IARA 2B8YA 1EKUA 2INTA 5IYDD 1IJZA 2Z3QA 2XQBA 4CNIC 1M4BA 1V7MV 3AYHA 1Y1VD 1RCBA 3HOWD 1BCNA 1Y1WD 1M48A 2LAGA 4MHLA 5D22A 2Q14A 4A3KD 1BGCA 4DKEA 3LB6A 2B91A 3HOUD 1RW5A 1HWHA 3DUHC 4GS7A 3HOXD 1CD9A 3HOVD 4A3GD 1ITLA 1CYLA 1PVHB 3HHCA 4NEMA 3IRHA 4FA8E 2Z3RA 1ITFA 1P9MB 1ITIA 1ALUA 3BPNA 1Y6KL 3PO3D 4NN5A 1BGDA
chains in the Genus database with same CATH homology


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