1Y1WD

Complete rna polymerase ii elongation complex
Total Genus 41
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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
41
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 Transcription,transferase/dna-rna hybrid
molecule keywords 5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*GP*CP*CP*TP*GP*GP*TP*CP*AP
publication title Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS
pubmed doi rcsb
total genus 41
structure length 177
sequence length 218
ec nomenclature
pdb deposition date 2004-11-19

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; 1y1wD02
4A3JD 5IYCD 5FLMD 3I4ND 5IP7D 4A3ID 3HOYD 4A3BD 2R92D 3AYHA 2VUMD 2R93D 4BXXD 5IYDD 2C35A 4A3LD 3HOUD 1Y1VD 2JA7D 3HOVD 1WCMD 4BY1D 3H3VE 2B63D 3PO3D 2JA5D 3FKID 3I4MD 5IP9D 1Y1WD 5C44D 3HOXD 4A3MD 5C3ED 1Y14A 4A3FD 3HOWD 2JA6D 5IYBD 5C4XD 4A3CD 4BBSD 4A3GD 3H0GD 3PO2D 4A3DD 4A3ED 4A93D 4BBRD 2R7ZD 3HOZD 4BY7D 2JA8D 4A3KD
chains in the Genus database with same CATH superfamily
1F45B 2XQBA 3O7PA 4LDSA 4GC0A 1PV7A 2ILKA 1BGCA 1ITFA 3SE3B 5A2NA 4LRLA 3L5XA 3HOWD 5C4XD 3PO2D 3PIWA 4DOHA 5KNHI 5C7XA 5LQBA 4PS4A 1AU1A 1PW6A 3NCBA 1SCFA 3EJJA 2B8YA 1FYHA 3OG6A 1RCBA 3UF2A 1CN4C 2HYMB 1GA3A 4TPGA 5IP9D 1EXZA 1BBNA 4PYPA 4NI7A 4TPHA 4A3GD 1EMRA 3UEZE 1IL6A 3B5KA 3S9DA 1I1RB 4DKCA 3BESL 1N1FA 3QAZA 2XUTA 4ZYRA 1M4BA 3PO3D 2B8XA 2O6IA 3UX9A 3DLQI 4YB9D 4Q65A 1NBPA 4A3JD 3QB7A 2GMFA 1BGDA 4U4WA 4D2CA 4ZF7A 1CSGA 1BUYA 4X51A 1LKIA 5IYBD 1YKBA 4J4LC 3HHCA 1HIKA 1Y6NL 1Y6ML 3N06A 1V7NV 1ITIA 2B5IA 2B63D 4XNJA 4YPGC 1JLIA 3HOXD 2B90A 1WU3I 3IRHA 3H0GD 5EQGA 4EXPA 4IKZA 3HMXB 4ZW9A 3HHRA 3N0PA 1IK0A 4IKYA 4ZWCA 1IJZA 1M48A 1Y1VD 4ZS7A 1WCMD 2E9WC 1CYLA 4D2DA 1KF9A 3FKID 2KZ1A 1Y1WD 4LEPA 5C44D 3UF5A 4YBQA 2CFPA 4A3CD 1GNCA 1M49A 2O27A 3G6DA 4BBRD 1V7MV 4GBYA 2JA8D 4YDYI 3I4ND 4A3ID 3HOYD 4A3BD 3LB6A 4OH3A 2R92D 4IKVA 5D58A 3EW3A 5TS9A 3QT2C 1PVHB 4YQXA 1Y14A 4MHLA 5D22A 1ILKA 4APSA 2LMSA 1PW4A 4NEJA 3O7QA 1ALUA 4NN7A 5EQHA 4J05A 4O9HA 4GBZA 4BXXD 1PY2A 2LAGA 3HOVD 1F6FA 3QWRB 1FG9A 3I4MD 5FUCA 5C3ED 1CNT1 2L3OA 1VLKA 1HGUA 3D85C 2B91A 1HIJA 1PGRA 1D9CA 3DI2A 3AYHA 2VUMD 2Q98A 5D59A 1RFBA 4NKQC 4UVMA 1HUWA 3H3VE 1PV6A 3G9VB 4GRWA 1ITLA 3NCCA 4RS1A 1D9GA 3BPOA 4A93D 3VA2A 1M4AA 1Z92A 4A3DD 4GS7A 2D48A 4U4TA 2B8ZA 4A3LD 3D87A 2Q7NB 5D6KA 2Y5YA 4YUEC 5GXBA 4NEMA 1RW5A 3OQ3A 4A3ED 1HZIA 3HOZD 2R93D 2Z3RA 1EERA 2ERJD 3DI3A 3MZGA 2INTA 1ETEA 4EXNA 2H24A 2JA5D 1BP3A 4A3MD 5L6YC 1J7VL 5D70A 2Q14A 1CD9A 3WDOA 3WCYI 4BBSD 1P9MB 4ZWBA 2CFQA 4FA8E 3DUHC 1IRLA 3NCEA 1M47A 3LB6B 4XNIA 1A7MA 2B8UA 2L3YA 4NN5A 1QVNA 4WRLB 3PIVA 2JA6D 3QB1A 1EKUA 2R7ZD 4QIQA 1HWHA 4I77Z 3NCFA 4JA3A 4DKEA 5IYCD 4A3KD 5D28B 5IYDD 2JA7D 3BPLA 3NPZA 4NI9A 4W6VA 3SE4B 3TGXB 3D48P 2IL6A 2O26A 4BY7D 5FLMD 1INRA 4OAAA 1AXIA 5IP7D 2OQPA 1M4CA 5D71A 1A22A 1IARA 3OG4A 2Z3QA 3DGCL 4JR9A 4A3FD 3L5WI 1BGEA 4IKXA 4NN6A 4IKWA 4DKFA 5E4EA 1LK3A 1ITMA 3Q1SI 2C35A 4TPJA 1B5LA 5EQIA 1BCNA 4CNIC 1RHGA 2V8NA 2D9QA 2CYKA 4IU9A 4O6KA 4U4VA 1AX8A 5C65A 2PSMA 1Z7CA 5A2OA 4JREA 4DKDA 1HULA 3HOUD 5FHXA 1HWGA 3BPNA 1LQSL 4BY1D 4D2BA 1M4RA 3INKC 1Y6KL 4Z5RD 1EVSA 4IU8A 5D72A
chains in the Genus database with same CATH topology
1Y6NL 4DKEA 1F45B 5IYCD 1Y6ML 3N06A 2XQBA 5LQBA 1V7NV 3DI2A 3AYHA 2VUMD 2Q98A 5D28B 1ITIA 2B5IA 5IYDD 1RFBA 4NKQC 2JA7D 2ILKA 1HUWA 3H3VE 2B63D 4YPGC 5D72A 1JLIA 3HOXD 1BGCA 1ITFA 3BPLA 3NPZA 2B90A 1WU3I 3G9VB 4GRWA 3SE3B 3HOWD 4LRLA 3L5XA 1ITLA 3IRHA 3NCCA 5C4XD 3H0GD 4RS1A 4NI9A 3PO2D 3PIWA 1D9GA 3BPOA 4EXPA 4DOHA 3SE4B 4A93D 5KNHI 3HMXB 5C7XA 3TGXB 3VA2A 4PS4A 3HHRA 1M4AA 1AU1A 2IL6A 1PW6A 2O26A 1SCFA 3D48P 3N0PA 1Z92A 3NCBA 4A3DD 4GS7A 1INRA 5FLMD 4BY7D 1AXIA 5IP7D 3EJJA 2D48A 2B8YA 2OQPA 1FYHA 2B8ZA 3OG6A 1RCBA 1M4CA 5D71A 4A3LD 1IJZA 1CN4C 1M48A 3D87A 2Q7NB 1Y1VD 3UF2A 4ZS7A 1WCMD 2HYMB 2E9WC 1CYLA 1GA3A 1A22A 1IARA 3OG4A 1KF9A 3FKID 2KZ1A 5IP9D 1Y1WD 1EXZA 5C44D 4YUEC 2Z3QA 3DGCL 3UF5A 4A3FD 1BBNA 4NEMA 3L5WI 4NI7A 1BGEA 4A3CD 1RW5A 4A3GD 1GNCA 3OQ3A 1EMRA 4A3ED 1M49A 1HZIA 3NCFA 2O27A 3G6DA 1IL6A 4NN6A 3UEZE 4BBRD 4A3KD 3HOZD 3B5KA 4DKFA 1V7MV 2R93D 2Z3RA 2JA8D 1EERA 4YDYI 3I4ND 3S9DA 4A3ID 3HOYD 4A3BD 3LB6A 5E4EA 2ERJD 3DI3A 1LK3A 1I1RB 2R92D 4DKCA 3BESL 1ITMA 3Q1SI 2C35A 3MZGA 1N1FA 4I77Z 1B5LA 2INTA 3QAZA 1ETEA 1M4BA 4EXNA 2H24A 3PO3D 3EW3A 2JA5D 1BP3A 2B8XA 1PVHB 3QT2C 5TS9A 1BCNA 4CNIC 4A3MD 5L6YC 1RHGA 2O6IA 4YQXA 1J7VL 1Y14A 4MHLA 5D70A 5D22A 1ILKA 2LMSA 2Q14A 2D9QA 3UX9A 1CD9A 2CYKA 3WCYI 4BBSD 1P9MB 4NEJA 1ALUA 4NN7A 3DLQI 4O6KA 1AX8A 4FA8E 3DUHC 2PSMA 4A3JD 1NBPA 1IRLA 1Z7CA 3NCEA 1M47A 3QB7A 4O9HA 2GMFA 3LB6B 1A7MA 1BGDA 2B8UA 2L3YA 4NN5A 4BXXD 1PY2A 1QVNA 4DKDA 1HULA 3HOUD 5FHXA 2LAGA 1HWGA 4ZF7A 3HOVD 4WRLB 1F6FA 3BPNA 1LQSL 4BY1D 3QWRB 1CSGA 1FG9A 3I4MD 3PIVA 1M4RA 1BUYA 5FUCA 4X51A 5C3ED 1LKIA 1CNT1 3INKC 2L3OA 2JA6D 1Y6KL 5IYBD 1VLKA 3QB1A 4Z5RD 1EVSA 1HGUA 3D85C 1YKBA 4J4LC 1EKUA 2B91A 1IK0A 1HIJA 2R7ZD 1PGRA 1HWHA 3HHCA 1HIKA 1D9CA
chains in the Genus database with same CATH homology


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