2JA6D

Cpd lesion containing rna polymerase ii elongation complex b
Total Genus 40
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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
40
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
molecule keywords DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
publication title CPD damage recognition by transcribing RNA polymerase II.
pubmed doi rcsb
total genus 40
structure length 177
sequence length 218
ec nomenclature
pdb deposition date 2006-11-23

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; 2ja6D02
5FLMD 3HOXD 4A3ID 3HOVD 2C35A 5IYDD 1Y1WD 2R93D 4A3GD 5C44D 3AYHA 4A3MD 4A3DD 4A3LD 3H3VE 2R92D 5IP9D 3HOUD 3HOYD 4A3KD 4A93D 5IYCD 2JA6D 5C3ED 5IP7D 3HOZD 4BBSD 4BY7D 2R7ZD 4A3BD 4BXXD 3PO3D 3H0GD 1Y1VD 1Y14A 2B63D 1WCMD 3FKID 4BBRD 4BY1D 2JA7D 2JA5D 3I4ND 4A3FD 4A3JD 2VUMD 5IYBD 5C4XD 4A3ED 3I4MD 3PO2D 3HOWD 2JA8D 4A3CD
chains in the Genus database with same CATH superfamily
1PVHB 3NCEA 3Q1SI 4PYPA 1LK3A 3TGXB 2HYMB 1P9MB 4YDYI 4IKXA 4ZS7A 2PSMA 4A3JD 4O9HA 1Y6ML 2CFPA 1JLIA 5A2NA 5C7XA 4NI9A 1BGEA 3PIWA 4APSA 4MHLA 1Y6KL 1INRA 2B91A 5D71A 1RFBA 3OG4A 1SCFA 1BGCA 4RS1A 3I4ND 3DLQI 1ILKA 5GXBA 3DGCL 4EXPA 4GS7A 2V8NA 5IP9D 3HOUD 3EJJA 4LRLA 4BY7D 3DUHC 3O7PA 2B63D 4NI7A 5C4XD 3BPNA 3L5WI 5D58A 2IL6A 5IYDD 3HOYD 1KF9A 3QB1A 1BCNA 4DOHA 2VUMD 2D9QA 1A22A 2CFQA 1PGRA 4W6VA 4XNIA 2C35A 1ALUA 3UF2A 1IJZA 4A3GD 4TPJA 4A3MD 3DI2A 3D87A 1D9GA 1EERA 4LDSA 1AU1A 3UX9A 1FG9A 4ZYRA 5A2OA 3BESL 1CYLA 2CYKA 4JR9A 4BY1D 3UEZE 1IRLA 4NN6A 1Z7CA 3EW3A 3INKC 1GA3A 3HHCA 4A3ED 4JA3A 1HWHA 2B8ZA 4DKFA 4A3LD 4UVMA 3LB6B 4NEJA 1CN4C 1M4RA 2XQBA 4FA8E 5C3ED 4BBSD 3PO3D 5L6YC 2JA7D 1PY2A 1YKBA 1PV7A 3HOVD 4WRLB 1CNT1 1M4BA 1LQSL 2Z3RA 4ZWCA 4J05A 1B5LA 5IYCD 4GBZA 4DKEA 1ETEA 4BBRD 1HWGA 2Q7NB 4IU8A 1RW5A 3N0PA 3HMXB 4O6KA 3I4MD 4JREA 3LB6A 4LEPA 1CSGA 2D48A 5LQBA 2B5IA 5C44D 4A3DD 5D6KA 1RHGA 5D59A 5E4EA 1NBPA 1ITLA 1HIJA 2JA6D 1AX8A 3L5XA 1M47A 3HOZD 3QWRB 1WCMD 3WDOA 5C65A 2O27A 2OQPA 4A3ID 4GBYA 1GNCA 4A93D 2LMSA 5IP7D 3UF5A 1M4CA 3IRHA 1Y14A 5EQHA 3NCFA 3D85C 4ZF7A 3PIVA 4A3CD 3HOXD 1HIKA 1HZIA 3DI3A 1M4AA 1V7MV 3AYHA 4YBQA 1HUWA 1LKIA 1PW4A 3H3VE 3HHRA 2R92D 3SE4B 5EQIA 3G9VB 4PS4A 1Z92A 2L3YA 3FKID 4EXNA 4CNIC 4DKCA 2B8UA 2B8XA 1F45B 4IKYA 2L3OA 1BP3A 3O7QA 4TPGA 2Z3QA 4D2CA 4U4WA 1I1RB 2Q14A 1M48A 5D22A 1ITMA 4NN5A 3BPLA 3HOWD 2O26A 4ZW9A 2ERJD 5TS9A 4ZWBA 3G6DA 1HGUA 5FHXA 3BPOA 1EVSA 1IK0A 4BXXD 1BUYA 1F6FA 5D70A 1Y6NL 1ITFA 3VA2A 1WU3I 1FYHA 4U4VA 4Z5RD 5FLMD 1HULA 2B8YA 4IKZA 1BGDA 1Y1WD 1BBNA 1VLKA 4OH3A 2GMFA 3QT2C 1EMRA 4GC0A 3NCBA 3SE3B 1IL6A 3H0GD 4A3FD 2Y5YA 2Q98A 1IARA 3PO2D 4I77Z 2JA8D 1EXZA 3NPZA 1N1FA 3OG6A 1V7NV 2R93D 3D48P 5D72A 1D9CA 4NKQC 3B5KA 2LAGA 2ILKA 1J7VL 2JA5D 1PV6A 2O6IA 4X51A 5KNHI 2B90A 1PW6A 1QVNA 1M49A 4A3KD 4NN7A 4GRWA 4IU9A 4A3BD 4QIQA 1EKUA 4TPHA 3OQ3A 5EQGA 4YUEC 3N06A 5FUCA 4U4TA 4D2BA 4IKVA 2E9WC 2KZ1A 4YQXA 3WCYI 3NCCA 4Q65A 3S9DA 1AXIA 4NEMA 2XUTA 3QB7A 1A7MA 2INTA 4OAAA 4YPGC 4XNJA 1CD9A 4J4LC 2R7ZD 1Y1VD 2H24A 5D28B 3MZGA 1RCBA 3QAZA 1ITIA 4D2DA 4IKWA 4DKDA 5IYBD 4YB9D
chains in the Genus database with same CATH topology
5FLMD 1HULA 4A3ID 2B8YA 2C35A 1BGDA 1PVHB 3NCEA 1ALUA 1Y1WD 3Q1SI 3UF2A 1IJZA 4A3GD 1BBNA 1VLKA 1LK3A 3DI2A 4A3MD 3TGXB 1GNCA 2HYMB 1P9MB 2GMFA 3QT2C 3D87A 1EMRA 1D9GA 1EERA 1AU1A 3NCBA 1FG9A 3UX9A 4A93D 3SE3B 2LMSA 3BESL 4YDYI 1CYLA 2CYKA 5IP7D 3UF5A 1IL6A 4ZS7A 1M4CA 3IRHA 3H0GD 1Y14A 4BY1D 3UEZE 1IRLA 3NCFA 4NN6A 2PSMA 1Z7CA 4A3FD 4A3JD 3EW3A 3INKC 3D85C 4O9HA 3HHCA 1Y6ML 1IARA 2Q98A 1GA3A 4A3ED 4ZF7A 4I77Z 3PO2D 3PIVA 2JA8D 4A3CD 1EXZA 1JLIA 3NPZA 1N1FA 3HOXD 5C7XA 1HIKA 1HZIA 3OG6A 1V7NV 3DI3A 1M4AA 2R93D 1V7MV 4NI9A 1HWHA 2B8ZA 4DKFA 3AYHA 4A3LD 1BGEA 3D48P 1HUWA 1LKIA 3PIWA 3H3VE 4MHLA 3HHRA 2R92D 1Y6KL 3LB6B 1INRA 4NEJA 3SE4B 3G9VB 1CN4C 5D72A 2B91A 1M4RA 2XQBA 5D71A 1RFBA 4FA8E 5C3ED 4PS4A 4BBSD 1D9CA 4NKQC 1Z92A 3PO3D 3B5KA 2LAGA 3OG4A 5L6YC 2L3YA 2JA7D 2ILKA 3FKID 1J7VL 1PY2A 4EXNA 4CNIC 1SCFA 1BGCA 4DKCA 4RS1A 2JA5D 3I4ND 2B8UA 2B8XA 2O6IA 1ILKA 1F45B 3DLQI 1YKBA 4X51A 3DGCL 2L3OA 5KNHI 4EXPA 2B90A 1BP3A 4GS7A 3HOVD 4WRLB 1CNT1 1PW6A 1M4BA 2Z3QA 1LQSL 2Z3RA 5IP9D 3HOUD 1QVNA 1B5LA 1I1RB 3EJJA 1M49A 2Q14A 4LRLA 4A3KD 4NN7A 5IYCD 1M48A 4GRWA 4DKEA 4BY7D 1ETEA 3DUHC 4A3BD 5D22A 1ITMA 1EKUA 3OQ3A 2B63D 4BBRD 1HWGA 4YUEC 2Q7NB 3N06A 1RW5A 4NN5A 3N0PA 3HMXB 5FUCA 4O6KA 4NI7A 5C4XD 3BPNA 3I4MD 3BPLA 3L5WI 3HOWD 2O26A 2E9WC 2KZ1A 2IL6A 2ERJD 3LB6A 5TS9A 5IYDD 4YQXA 1CSGA 2D48A 5LQBA 2B5IA 3WCYI 3G6DA 5C44D 3NCCA 4A3DD 3S9DA 1HGUA 1AXIA 4NEMA 3HOYD 5FHXA 3BPOA 1KF9A 1RHGA 5E4EA 3QB7A 1A7MA 3QB1A 1NBPA 2INTA 1ITLA 1HIJA 1EVSA 4YPGC 2JA6D 1IK0A 1BCNA 1AX8A 3L5XA 1M47A 3HOZD 1CD9A 4J4LC 4DOHA 2R7ZD 4BXXD 1BUYA 1Y1VD 2H24A 3QWRB 1F6FA 1WCMD 3MZGA 5D28B 5D70A 1Y6NL 1RCBA 1ITFA 3QAZA 2VUMD 2D9QA 3VA2A 1ITIA 2O27A 1A22A 1WU3I 1FYHA 4DKDA 5IYBD 2OQPA 1PGRA 4Z5RD
chains in the Genus database with same CATH homology


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