2JA8D

Cpd lesion containing rna polymerase ii elongation complex d
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; 2ja8D02
4A3ID 4A3JD 2JA5D 4BY7D 5IYBD 3PO2D 3AYHA 4BBSD 4A3FD 4BXXD 1Y1VD 1WCMD 5C44D 2VUMD 3HOYD 5IYDD 4A3BD 2B63D 3PO3D 2C35A 4A3GD 2R7ZD 3HOVD 4A3KD 1Y14A 2R92D 3HOWD 2JA7D 4A3DD 3HOUD 3H0GD 3I4ND 3FKID 4A3MD 2JA8D 4A93D 3H3VE 2R93D 4A3CD 2JA6D 3HOXD 4A3LD 5IYCD 5IP7D 3HOZD 4BBRD 3I4MD 1Y1WD 5C4XD 4BY1D 5C3ED 5FLMD 5IP9D 4A3ED
chains in the Genus database with same CATH superfamily
2Q14A 3SE3B 1M4BA 4LEPA 3NCBA 2B63D 2R7ZD 2R92D 1IK0A 1RHGA 3QAZA 4ZYRA 5KNHI 3QT2C 3UF5A 4BBRD 1A22A 3L5XA 2Y5YA 5C3ED 3OG6A 5FLMD 1M4CA 1RCBA 1V7NV 1BP3A 2D9QA 4LDSA 1Y14A 4IU8A 1ITLA 4ZWBA 5L6YC 4ZWCA 1M48A 1RW5A 5E4EA 3INKC 5IYCD 1PW4A 1IL6A 5D72A 5EQGA 1IRLA 3NCEA 1BUYA 1N1FA 2L3OA 4NN5A 4IKVA 5C44D 1WCMD 2VUMD 3PO3D 1M49A 5EQHA 3O7PA 1CYLA 2CFPA 3H3VE 1M4RA 3G6DA 4TPHA 3DGCL 3B5KA 4IU9A 3EJJA 2XQBA 2Q7NB 4GS7A 3UX9A 3BPLA 4U4WA 4A3KD 1BCNA 2GMFA 2JA7D 1M4AA 5A2OA 1PVHB 4OAAA 3DUHC 2B5IA 5EQIA 4NEJA 3LB6A 4D2BA 2O27A 1WU3I 4APSA 1M47A 5GXBA 1Y1VD 2Z3RA 2D48A 4TPJA 2KZ1A 3S9DA 1HIJA 4GBYA 1INRA 4IKWA 1PV7A 1GA3A 3HHCA 1JLIA 4Z5RD 4TPGA 4NN6A 5D28B 2Z3QA 5A2NA 4A3FD 4O6KA 2C35A 2ILKA 3HOVD 2XUTA 1NBPA 5TS9A 1EKUA 1Y6KL 3D48P 3I4ND 1HWGA 1HWHA 1D9GA 2Q98A 4OH3A 1A7MA 1IARA 5IP9D 1LK3A 3OG4A 3BPOA 1V7MV 4A3GD 1BBNA 3PIWA 4RS1A 5D6KA 2H24A 5D59A 4EXNA 4IKYA 3OQ3A 1ALUA 4A3CD 1BGEA 1Y6ML 3O7QA 1AX8A 1P9MB 5FHXA 1FYHA 5FUCA 3HOYD 1ITFA 2B8YA 3HMXB 1HGUA 3TGXB 4D2DA 2B90A 5D22A 1Y1WD 1VLKA 3NCCA 4YDYI 2L3YA 2OQPA 4YQXA 3N0PA 4XNIA 2V8NA 1PGRA 1CN4C 1CSGA 1BGDA 1J7VL 4O9HA 2B91A 4JA3A 4DKFA 4A3JD 1ITMA 4XNJA 4I77Z 3BESL 4JREA 3QB7A 4WRLB 3HOWD 4A3DD 3HOUD 3H0GD 2O6IA 2JA8D 3D87A 2JA6D 3WCYI 4Q65A 2JA5D 4U4TA 4DKDA 2B8XA 4W6VA 4YUEC 3QWRB 3SE4B 4J4LC 4ZF7A 2ERJD 1LQSL 1HULA 1PY2A 4A93D 2R93D 4ZS7A 3D85C 4NI9A 4YPGC 4BY1D 2E9WC 1F45B 4BY7D 3QB1A 1BGCA 4BBSD 3DLQI 2PSMA 1EXZA 1EERA 5C7XA 4NI7A 4YBQA 1IJZA 4MHLA 4J05A 2LMSA 3IRHA 3I4MD 5D71A 4GRWA 1EVSA 4D2CA 4ZW9A 1Z92A 4YB9D 1KF9A 5IYDD 4U4VA 3HHRA 4GC0A 4UVMA 1F6FA 2CFQA 3FKID 1AU1A 3HOXD 1QVNA 5IP7D 1PW6A 4JR9A 5C65A 1RFBA 1AXIA 3NPZA 1SCFA 3EW3A 3NCFA 4DOHA 3AYHA 3Q1SI 2IL6A 4DKCA 4A3BD 2CYKA 1YKBA 4NEMA 1HZIA 2B8ZA 2HYMB 1I1RB 1ILKA 3DI3A 5D58A 4GBZA 4CNIC 4DKEA 3UEZE 4PS4A 1D9CA 1B5LA 4A3ID 3PO2D 4IKXA 1CD9A 2B8UA 3PIVA 3BPNA 1EMRA 1FG9A 4NN7A 3MZGA 3VA2A 2O26A 1HUWA 3L5WI 4A3MD 4A3LD 3HOZD 3UF2A 3WDOA 1HIKA 1Y6NL 3G9VB 5IYBD 3LB6B 4PYPA 4BXXD 3N06A 1LKIA 5D70A 1GNCA 1PV6A 4IKZA 2LAGA 1CNT1 4LRLA 1ETEA 4QIQA 1Z7CA 4FA8E 3DI2A 4EXPA 2INTA 4NKQC 5C4XD 1ITIA 5LQBA 4X51A 4A3ED
chains in the Genus database with same CATH topology
2Q14A 1KF9A 1M47A 3SE3B 2L3YA 2OQPA 1M4BA 1Y1VD 5IYDD 3NCBA 2B63D 4X51A 4YQXA 2Z3RA 3HHRA 2D48A 3N0PA 2R7ZD 2R92D 2KZ1A 3S9DA 1IK0A 1HIJA 1F6FA 1PGRA 1RHGA 3QAZA 1CN4C 1INRA 1BGDA 1CSGA 5KNHI 3FKID 1J7VL 1AU1A 3QT2C 4O9HA 3UF5A 2B91A 3HOXD 1GA3A 3HHCA 1QVNA 1JLIA 5IP7D 4Z5RD 1PW6A 4BBRD 1A22A 4NN6A 1RFBA 1AXIA 3L5XA 5D28B 3NPZA 1SCFA 2Z3QA 4DKFA 3OG6A 5FLMD 5C3ED 4A3JD 1ITMA 3EW3A 1M4CA 1RCBA 3NCFA 4I77Z 4DOHA 3BESL 1V7NV 3AYHA 3Q1SI 1BP3A 4A3FD 4O6KA 2IL6A 2D9QA 4DKCA 4A3BD 2CYKA 1YKBA 4NEMA 2C35A 1HZIA 2ILKA 3QB7A 3HOVD 4WRLB 2B8ZA 2HYMB 1NBPA 5TS9A 1Y14A 3HOWD 1ITLA 1I1RB 1ILKA 1EKUA 3HOUD 4A3DD 1Y6KL 5L6YC 3D48P 3DI3A 2O6IA 3H0GD 1HWGA 1HWHA 1M48A 1RW5A 2JA8D 3I4ND 3D87A 5E4EA 2JA6D 3INKC 3WCYI 1D9GA 2Q98A 5IYCD 4CNIC 1IL6A 4DKEA 5D72A 3UEZE 1A7MA 1IARA 1IRLA 3NCEA 4PS4A 1BUYA 5IP9D 1LK3A 1D9CA 1B5LA 1N1FA 2L3OA 4A3ID 2JA5D 3PO2D 1CD9A 4NN5A 4DKDA 3OG4A 2B8XA 2B8UA 4YUEC 1WCMD 5C44D 2VUMD 3PIVA 3PO3D 3BPNA 3QWRB 3BPOA 1M49A 3SE4B 1V7MV 4A3GD 1EMRA 4J4LC 1BBNA 4ZF7A 3PIWA 1FG9A 4NN7A 3MZGA 4RS1A 3VA2A 2H24A 2O26A 2ERJD 1LQSL 4EXNA 1HULA 1HUWA 1CYLA 1PY2A 3OQ3A 3L5WI 4A3MD 4A93D 3H3VE 1ALUA 2R93D 4A3CD 4ZS7A 1M4RA 3D85C 4A3LD 3HOZD 3UF2A 4NI9A 1BGEA 4YPGC 1Y6ML 3G6DA 1HIKA 4BY1D 1AX8A 2E9WC 3DGCL 3B5KA 1F45B 1P9MB 4BY7D 3QB1A 1Y6NL 5FHXA 3G9VB 1BGCA 5IYBD 4BBSD 3DLQI 3LB6B 1FYHA 4BXXD 3EJJA 2PSMA 2XQBA 5FUCA 1EXZA 4GS7A 2Q7NB 3HOYD 1ITFA 2B8YA 3HMXB 3UX9A 3N06A 1HGUA 1EERA 1LKIA 3BPLA 5D70A 5C7XA 4A3KD 1GNCA 1BCNA 2GMFA 2JA7D 4NI7A 1M4AA 1PVHB 2LAGA 3TGXB 3DUHC 1CNT1 4LRLA 1IJZA 4MHLA 2B5IA 1ETEA 2LMSA 1Z7CA 2B90A 3IRHA 4FA8E 3DI2A 3I4MD 5D22A 4NEJA 2INTA 4NKQC 3LB6A 5D71A 4EXPA 1Y1WD 1VLKA 4GRWA 5C4XD 2O27A 5LQBA 1EVSA 1ITIA 1WU3I 3NCCA 4A3ED 4YDYI 1Z92A
chains in the Genus database with same CATH homology


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