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


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