3PO3D

Arrested rna polymerase ii reactivation intermediate
Total Genus 53
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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
53
sequence length
218
structure length
177
Chain Sequence
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 tags Transferase/dna/rna
molecule keywords DNA-directed RNA polymerase II subunit RPB1
publication title Structural basis of RNA polymerase II backtracking, arrest and reactivation.
pubmed doi rcsb
source organism Saccharomyces cerevisiae
total genus 53
structure length 177
sequence length 218
ec nomenclature
pdb deposition date 2010-11-21

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; 3po3D02
3HOWD 2JA5D 2R7ZD 5IP9D 2R92D 3HOYD 4BXXD 1WCMD 3HOVD 3AYHA 3HOXD 4BBSD 4BY7D 2R93D 3HOZD 5C4XD 3H3VE 5IYBD 5IYCD 4A3BD 4A3CD 2JA6D 3HOUD 2B63D 4BBRD 2C35A 1Y1VD 3H0GD 3FKID 3I4ND 4BY1D 3PO2D 3PO3D 1Y1WD 4A3KD 5C3ED 4A93D 4A3DD 4A3JD 4A3FD 5FLMD 5IYDD 3I4MD 5IP7D 5C44D 4A3GD 4A3ID 1Y14A 2JA7D 4A3LD 2JA8D 2VUMD 4A3ED 4A3MD
chains in the Genus database with same CATH superfamily
1IK0A 2Q14A 1Z7CA 4IKWA 4WRLB 5C65A 1BUYA 2PSMA 3OQ3A 2B8YA 3QB7A 4CNIC 2B91A 2Q98A 2D48A 3BPNA 1B5LA 1QVNA 5FUCA 2LMSA 1EERA 3S9DA 3HOWD 4ZF7A 1RHGA 1IRLA 5D59A 3N06A 1V7MV 2CFPA 3G9VB 5IYBD 4OH3A 3FKID 1KF9A 1PV6A 2L3OA 5IP7D 3WCYI 4YB9D 1M4BA 5GXBA 4TPJA 2ILKA 4FA8E 4A3BD 1CD9A 1BP3A 2IL6A 5FHXA 5D6KA 2HYMB 3PO3D 3INKC 1FYHA 1PW6A 1CN4C 1VLKA 4D2DA 2O26A 4LRLA 2JA8D 4IKZA 3BESL 2Z3RA 2CYKA 3BPLA 4GBYA 4I77Z 1Y6KL 1GNCA 1HWGA 1ITLA 4IU9A 3QWRB 3OG6A 4NN5A 2Z3QA 4DKEA 2L3YA 4RS1A 3PO2D 4DKFA 4A3FD 4YBQA 3G6DA 4A3ED 3L5WI 2H24A 3PIVA 4X51A 3DI2A 1EXZA 2B8XA 3NCBA 3HOXD 4ZW9A 5D71A 4XNIA 2B8ZA 4JA3A 5KNHI 4EXPA 2B8UA 3WDOA 1J7VL 2GMFA 3UEZE 4U4VA 3HOVD 1ILKA 1LKIA 4GS7A 1M4RA 4J4LC 4APSA 1IJZA 1Y6ML 3H0GD 1N1FA 1HIKA 4A93D 4Q65A 1M4CA 4IKXA 1GA3A 1IL6A 4QIQA 1ITMA 1EKUA 1WCMD 4W6VA 4BBSD 4YPGC 3UF2A 3HHCA 4ZYRA 3MZGA 3B5KA 1I1RB 3UX9A 1Y14A 3NCCA 3DI3A 4A3MD 3QB1A 1ALUA 3VA2A 1FG9A 1M48A 4D2BA 3L5XA 2O6IA 2C35A 1Y1WD 4PYPA 4NN7A 2XUTA 1RW5A 4YDYI 4A3LD 2XQBA 1CYLA 2B5IA 2JA5D 2OQPA 4IU8A 3LB6A 1NBPA 3QAZA 3EW3A 2JA6D 1HIJA 1PVHB 4Z5RD 1RFBA 2INTA 2O27A 4A3JD 2D9QA 5IYDD 4NI7A 1HUWA 1D9CA 2R7ZD 4ZWCA 2V8NA 2R93D 4NKQC 1ETEA 2Q7NB 1M4AA 4U4WA 1BCNA 1HWHA 3HOUD 1PY2A 1ITIA 1Y1VD 4TPGA 5TS9A 4O9HA 1Y6NL 4JREA 3O7QA 5EQIA 5C4XD 3Q1SI 3H3VE 1F45B 2ERJD 3DUHC 1BGCA 5E4EA 4TPHA 2KZ1A 3SE4B 5C44D 4A3ID 3BPOA 4OAAA 1P9MB 5EQHA 1JLIA 1CNT1 5IP9D 1Z92A 4BXXD 3HHRA 1CSGA 1M49A 1LK3A 4LEPA 4UVMA 4U4TA 3TGXB 1EMRA 4O6KA 5EQGA 4DKDA 4A3GD 4IKVA 2JA7D 4NEJA 1HGUA 4PS4A 4IKYA 3AYHA 4BY7D 3NCEA 3HOZD 5D72A 3D87A 4GC0A 1BBNA 4BBRD 1D9GA 4EXNA 5D70A 4BY1D 4NI9A 4ZWBA 4A3KD 4DKCA 3O7PA 1HZIA 3NPZA 4D2CA 1A7MA 4MHLA 1AU1A 1RCBA 2CFQA 1WU3I 1PGRA 1PV7A 1F6FA 1ITFA 5A2NA 1EVSA 4GRWA 3D85C 4J05A 5IYCD 1AX8A 5A2OA 4YUEC 5LQBA 1YKBA 4A3DD 1BGEA 3I4MD 3NCFA 4NEMA 3UF5A 5C7XA 1IARA 3EJJA 2VUMD 3LB6B 4XNJA 1AXIA 2R92D 3OG4A 3DGCL 5D22A 2B90A 1HULA 3DLQI 4YQXA 2B63D 2Y5YA 4NN6A 3QT2C 2LAGA 3SE3B 5D58A 5FLMD 1LQSL 4DOHA 1PW4A 1SCFA 5L6YC 1INRA 4LDSA 3HOYD 3PIWA 4JR9A 3HMXB 1M47A 4A3CD 1V7NV 1A22A 3I4ND 1BGDA 4GBZA 4ZS7A 5C3ED 3IRHA 2E9WC 3D48P 3N0PA 5D28B
chains in the Genus database with same CATH topology
2H24A 1HGUA 3PIVA 4X51A 1IK0A 4PS4A 2JA5D 3DI2A 2Q14A 1Z7CA 2OQPA 1EXZA 2B8XA 3NCBA 3AYHA 3HOXD 3NCEA 4BY7D 4WRLB 1BUYA 3LB6A 3HOZD 2PSMA 5D72A 1NBPA 3D87A 3QAZA 3EW3A 2JA6D 1BBNA 3OQ3A 1HIJA 1D9GA 2B8YA 5D71A 5D70A 4BBRD 4EXNA 4BY1D 4NI9A 3QB7A 4CNIC 1PVHB 4Z5RD 2B8ZA 1RFBA 2INTA 2O27A 4DKCA 4A3KD 5KNHI 2B91A 2D9QA 4A3JD 4EXPA 5IYDD 2Q98A 4NI7A 2B8UA 1HZIA 3NPZA 2D48A 1HUWA 1A7MA 4MHLA 1J7VL 3BPNA 1B5LA 1D9CA 1QVNA 2GMFA 1AU1A 5FUCA 3UEZE 1RCBA 2LMSA 1EERA 1WU3I 3S9DA 4ZF7A 1PGRA 3HOWD 2R7ZD 1RHGA 1IRLA 3N06A 2R93D 1F6FA 3HOVD 1V7MV 1ILKA 4NKQC 1ITFA 1ETEA 1LKIA 4GS7A 3G9VB 1M4RA 4J4LC 1EVSA 2Q7NB 1M4AA 4GRWA 3D85C 5IYBD 5IYCD 1BCNA 1IJZA 1AX8A 1HWHA 1PY2A 1Y6ML 3HOUD 1ITIA 3H0GD 1Y1VD 3FKID 1N1FA 4YUEC 5LQBA 1HIKA 1YKBA 1KF9A 2L3OA 4A93D 1M4CA 4A3DD 1BGEA 3I4MD 1GA3A 5IP7D 3WCYI 3NCFA 4NEMA 3UF5A 5C7XA 1IARA 1IL6A 5TS9A 3EJJA 2VUMD 4O9HA 1M4BA 1Y6NL 3LB6B 1ITMA 1EKUA 1AXIA 2R92D 1WCMD 3OG4A 4BBSD 2ILKA 3DGCL 5C4XD 3Q1SI 4FA8E 3H3VE 5D22A 4YPGC 2B90A 4A3BD 1F45B 1HULA 2ERJD 3DLQI 3UF2A 1CD9A 1BP3A 2IL6A 3HHCA 3DUHC 4YQXA 5FHXA 2B63D 1BGCA 5E4EA 2HYMB 4NN6A 2KZ1A 3PO3D 3INKC 3QT2C 1FYHA 1PW6A 1CN4C 2LAGA 3SE3B 3SE4B 1VLKA 5FLMD 1LQSL 3MZGA 2O26A 5C44D 4DOHA 3B5KA 4A3ID 1I1RB 3UX9A 3BPOA 4LRLA 1Y14A 1SCFA 5L6YC 2JA8D 1P9MB 1INRA 3NCCA 3DI3A 1JLIA 4A3MD 3BESL 4A3ED 2Z3RA 3QB1A 2CYKA 3BPLA 1CNT1 1ALUA 3VA2A 5IP9D 1FG9A 1Z92A 3HOYD 1M48A 1Y6KL 4I77Z 1HWGA 4BXXD 1GNCA 3L5XA 3HHRA 1ITLA 2O6IA 3PIWA 1CSGA 3HMXB 3QWRB 1M47A 1M49A 3OG6A 4NN5A 4A3CD 1LK3A 2Z3QA 4DKEA 1V7NV 1A22A 2C35A 3I4ND 1BGDA 3TGXB 1EMRA 2L3YA 4RS1A 3PO2D 4ZS7A 4O6KA 1Y1WD 5C3ED 3IRHA 2E9WC 4DKFA 4NN7A 4A3FD 4DKDA 4A3GD 3D48P 1RW5A 3N0PA 5D28B 4YDYI 3G6DA 2JA7D 4A3LD 2XQBA 1CYLA 2B5IA 4NEJA 3L5WI
chains in the Genus database with same CATH homology


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