2JA8D

Cpd lesion containing rna polymerase ii elongation complex d
Total Genus 40
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...