4RZZA

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp in complex with phosphate
Total Genus 158
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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
158
sequence length
439
structure length
439
Chain Sequence
b'RKIDPSRGATLGDGTPNDNDRIEIGPTQLAFSEWAAAGLQLPNLDRMREYRWKRLTQAIVDRGYGGLLMFDPLNIRYATDSTNMQLWNTHNPFRAVLLCADGYMVIWDYKNSPFLSKFNPLVREQRSGADLFYFDRGDKVDVQADVFANEVRVLMQDHAPGHTRLAVDKIMLHGLRALEAQGFEIMEGEEVTEKTRAIKGPDEILAMRCASHACETAVAEMEKFARAHVGDGKTSEDDIWAVLHAENIKRGGEWIETRLLASGPRTNPWFQECGPRITQKNEIIAFDTDLIGSYGICVDISRTWWIGDQKPRPDMVYAMQHAHEHIMTNMEMLKPGVMIPDLTANCHRLDDKFQAQKYGCLMHGVGLCDEWPLVAYPDKAVPGSYDYPLEPGMVLCVEAAVGEVGGDFSIKLEDQVLITEDGYENLTTYPFDAALMGLA'
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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.

molecule keywords Peptidase M24
molecule tags Lyase
source organism Silicibacter lacuscaerulensis iti-1157
publication title Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold.
pubmed doi rcsb
total genus 158
structure length 439
sequence length 439
chains with identical sequence B, C, D
ec nomenclature
pdb deposition date 2014-12-27

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00557 Peptidase_M24 Metallopeptidase family M24
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.350.10 Alpha Beta 3-Layer(aba) Sandwich Creatine Amidinohydrolase; Chain A, domain 1 Creatinase/prolidase N-terminal domain 4rzzA01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4rzzA02
4IKSA 2Q93A 4PV4A 1XGOA 2B3HA 2EVMA 2GG9A 2V3ZA 4IKTA 4A6VA 4Z7MA 2GZ5A 4FKCA 2GU7A 4IKUA 1CHMA 4MATA 3L7GA 5JHUA 1YVMA 1WLRA 4S00A 2P99A 3PKBA 3PKEA 3CTZA 2V3YA 1MATA 2EVOA 1R58A 1QXYA 2BB7A 2GG0A 2Q8KA 4ZWUA 5CDLA 4PNCA 2ADUA 3BIPA 3CB5A 5D6EA 2MATA 2NQ6A 1WBQA 4U6EA 5D6FA 4KM3A 2G6PA 3PKAA 5CNXA 3PN9A 2GG5A 4U1BA 1B6AA 3PEBA 1R5HA 2GGBA 4U6CA 3RORA 5E5BA 1WY2A 3TAVA 4U70A 1KP0A 2BN7A 5CE6A 2B3KA 2GTXA 1B59A 2Q94A 1XGNA 2BHCA 3FMQA 3IU9A 3Q6DA 2EVCA 2P9AA 2HOWA 4ZWOA 4QR8A 4FLIA 3OVKA 5JFRA 1C23A 2Q95A 1KQ0A 2EA2A 3O5VA 1QXWA 1N51A 3MR1A 1R5GA 4FO8A 2DFIA 4A6WA 4RZYA 4ZNGA 1WKMA 2Q96A 2BWSA 2EA4A 2GA2A 1XGMA 3BITA 1YW9A 2GU4A 5CDVA 3IU7A 5CIKA 3RVAA 4ZWPA 4IKRA 2BWVA 4R60A 3S6BA 4FLJA 3D27A 2BWWA 4HXXA 1BN5A 5FCHA 1YW8A 2GU5A 4U6JA 1A16A 3FM3A 1C27A 4IPAA 1C21A 5E2CA 3OOOA 3QOCA 2GG7A 2GG3A 2BHAA 3I7MA 2BWXA 2V3XA 2BWYA 5CDEA 4B28A 4FLLA 4U6ZA 4EGEA 2P98A 4S2TP 4RGZ1 1BOAA 4FUKA 1C22A 3IL0A 2GG2A 2V6CA 4FO7A 2B3LA 4U73A 1Y1NA 1M35A 3BIQA 1QZYA 3CB6A 1XGSA 2OKNA 3FMRA 4U71A 1WL9A 4IF7A 2BWUA 1YW7A 2GU6A 3MATA 1C24A 1WN1A 5CLSA 2ZSGA 1XNZA 4FLKA 4IDYA 2BWTA 3MX6A 1WL6A 1PV9A 3IG4A 4S01A 1QXZA 4OOKA 4U69A 2BHDA 1YJ3A 4U75A 1KQ9A 2IW2A 3PKCA 2GGCA 2BHBA 5FCFA 3PKDA 1W7VA 2BH3A 3IU8A 3L24A 5JI6A 4S2RP 4RZZA 1W2MA 4IECA 2NQ7A 1O0XA 4IU6A 4U6WA 2GG8A 1JAWA 2OAZA 4JUQA 2Q92A 4U76A 3TB5A
chains in the Genus database with same CATH superfamily
4IKSA 2Q93A 4PV4A 1XGOA 2B3HA 2EVMA 2GG9A 2V3ZA 4IKTA 4A6VA 4Z7MA 2GZ5A 4FKCA 2GU7A 4IKUA 1CHMA 4MATA 3L7GA 5JHUA 1YVMA 1WLRA 4S00A 2P99A 3PKBA 3PKEA 3CTZA 2V3YA 1MATA 2EVOA 1R58A 1QXYA 2BB7A 2GG0A 2Q8KA 4ZWUA 5CDLA 4PNCA 2ADUA 3BIPA 3CB5A 5D6EA 2MATA 2NQ6A 1WBQA 4U6EA 5D6FA 4KM3A 2G6PA 3PKAA 5CNXA 3PN9A 2GG5A 4U1BA 1B6AA 3PEBA 1R5HA 2GGBA 4U6CA 3RORA 5E5BA 1WY2A 3TAVA 4U70A 1KP0A 2BN7A 5CE6A 2B3KA 2GTXA 1B59A 2Q94A 1XGNA 2BHCA 3FMQA 3IU9A 3Q6DA 2EVCA 2P9AA 2HOWA 4ZWOA 4QR8A 4FLIA 3OVKA 5JFRA 1C23A 2Q95A 1KQ0A 2EA2A 3O5VA 1QXWA 1N51A 3MR1A 1R5GA 4FO8A 2DFIA 4A6WA 4RZYA 4ZNGA 1WKMA 2Q96A 2BWSA 2EA4A 2GA2A 1XGMA 3BITA 1YW9A 2GU4A 5CDVA 3IU7A 5CIKA 3RVAA 4ZWPA 4IKRA 2BWVA 4R60A 3S6BA 4FLJA 3D27A 2BWWA 4HXXA 1BN5A 5FCHA 1YW8A 2GU5A 4U6JA 1A16A 3FM3A 1C27A 4IPAA 1C21A 5E2CA 3OOOA 3QOCA 2GG7A 2GG3A 2BHAA 3I7MA 2BWXA 2V3XA 2BWYA 5CDEA 4B28A 4FLLA 4U6ZA 4EGEA 2P98A 4S2TP 4RGZ1 1BOAA 4FUKA 1C22A 3IL0A 2GG2A 2V6CA 4FO7A 2B3LA 4U73A 1Y1NA 1M35A 3BIQA 1QZYA 3CB6A 1XGSA 2OKNA 3FMRA 4U71A 1WL9A 4IF7A 2BWUA 1YW7A 2GU6A 3MATA 1C24A 1WN1A 5CLSA 2ZSGA 1XNZA 4FLKA 4IDYA 2BWTA 3MX6A 1WL6A 1PV9A 3IG4A 4S01A 1QXZA 4OOKA 4U69A 2BHDA 1YJ3A 4U75A 1KQ9A 2IW2A 3PKCA 2GGCA 2BHBA 5FCFA 3PKDA 1W7VA 2BH3A 3IU8A 3L24A 5JI6A 4S2RP 4RZZA 1W2MA 4IECA 2NQ7A 1O0XA 4IU6A 4U6WA 2GG8A 1JAWA 2OAZA 4JUQA 2Q92A 4U76A 3TB5A
chains in the Genus database with same CATH topology
4IKSA 2Q93A 4PV4A 1XGOA 2B3HA 2EVMA 2GG9A 2V3ZA 4IKTA 4A6VA 4Z7MA 2GZ5A 4FKCA 2GU7A 4IKUA 1CHMA 4MATA 3L7GA 5JHUA 1YVMA 1WLRA 4S00A 2P99A 3PKBA 3PKEA 3CTZA 2V3YA 1MATA 2EVOA 1R58A 1QXYA 2BB7A 2GG0A 2Q8KA 4ZWUA 5CDLA 4PNCA 2ADUA 3BIPA 3CB5A 5D6EA 2MATA 2NQ6A 1WBQA 4U6EA 5D6FA 4KM3A 2G6PA 3PKAA 5CNXA 3PN9A 2GG5A 4U1BA 1B6AA 3PEBA 1R5HA 2GGBA 4U6CA 3RORA 5E5BA 1WY2A 3TAVA 4U70A 1KP0A 2BN7A 5CE6A 2B3KA 2GTXA 1B59A 2Q94A 1XGNA 2BHCA 3FMQA 3IU9A 3Q6DA 2EVCA 2P9AA 2HOWA 4ZWOA 4QR8A 4FLIA 3OVKA 5JFRA 1C23A 2Q95A 1KQ0A 2EA2A 3O5VA 1QXWA 1N51A 3MR1A 1R5GA 4FO8A 2DFIA 4A6WA 4RZYA 4ZNGA 1WKMA 2Q96A 2BWSA 2EA4A 2GA2A 1XGMA 3BITA 1YW9A 2GU4A 5CDVA 3IU7A 5CIKA 3RVAA 4ZWPA 4IKRA 2BWVA 4R60A 3S6BA 4FLJA 3D27A 2BWWA 4HXXA 1BN5A 5FCHA 1YW8A 2GU5A 4U6JA 1A16A 3FM3A 1C27A 4IPAA 1C21A 5E2CA 3OOOA 3QOCA 2GG7A 2GG3A 2BHAA 3I7MA 2BWXA 2V3XA 2BWYA 5CDEA 4B28A 4FLLA 4U6ZA 4EGEA 2P98A 4S2TP 4RGZ1 1BOAA 4FUKA 1C22A 3IL0A 2GG2A 2V6CA 4FO7A 2B3LA 4U73A 1Y1NA 1M35A 3BIQA 1QZYA 3CB6A 1XGSA 2OKNA 3FMRA 4U71A 1WL9A 4IF7A 2BWUA 1YW7A 2GU6A 3MATA 1C24A 1WN1A 5CLSA 2ZSGA 1XNZA 4FLKA 4IDYA 2BWTA 3MX6A 1WL6A 1PV9A 3IG4A 4S01A 1QXZA 4OOKA 4U69A 2BHDA 1YJ3A 4U75A 1KQ9A 2IW2A 3PKCA 2GGCA 2BHBA 5FCFA 3PKDA 1W7VA 2BH3A 3IU8A 3L24A 5JI6A 4S2RP 4RZZA 1W2MA 4IECA 2NQ7A 1O0XA 4IU6A 4U6WA 2GG8A 1JAWA 2OAZA 4JUQA 2Q92A 4U76A 3TB5A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4IKS A;  2Q93 A;  4PV4 A;  1XGO A;  2B3H A;  2EVM A;  2GG9 A;  2V3Z A;  4IKT A;  4A6V A;  4Z7M A;  2GZ5 A;  4FKC A;  2GU7 A;  4IKU A;  1CHM A;  4MAT A;  3L7G A;  5JHU A;  1YVM A;  1WLR A;  4S00 A;  2P99 A;  3PKB A;  3PKE A;  3CTZ A;  2V3Y A;  1MAT A;  2EVO A;  1R58 A;  1QXY A;  2BB7 A;  2GG0 A;  2Q8K A;  4ZWU A;  5CDL A;  4PNC A;  2ADU A;  3BIP A;  3CB5 A;  5D6E A;  2MAT A;  2NQ6 A;  1WBQ A;  4U6E A;  5D6F A;  4KM3 A;  2G6P A;  3PKA A;  5CNX A;  3PN9 A;  2GG5 A;  4U1B A;  1B6A A;  3PEB A;  1R5H A;  2GGB A;  4U6C A;  3ROR A;  5E5B A;  1WY2 A;  3TAV A;  4U70 A;  1KP0 A;  2BN7 A;  5CE6 A;  2B3K A;  2GTX A;  1B59 A;  2Q94 A;  1XGN A;  2BHC A;  3FMQ A;  3IU9 A;  3Q6D A;  2EVC A;  2P9A A;  2HOW A;  4ZWO A;  4QR8 A;  4FLI A;  3OVK A;  5JFR A;  1C23 A;  2Q95 A;  1KQ0 A;  2EA2 A;  3O5V A;  1QXW A;  1N51 A;  3MR1 A;  1R5G A;  4FO8 A;  2DFI A;  4A6W A;  4RZY A;  4ZNG A;  1WKM A;  2Q96 A;  2BWS A;  2EA4 A;  2GA2 A;  1XGM A;  3BIT A;  1YW9 A;  2GU4 A;  5CDV A;  3IU7 A;  5CIK A;  3RVA A;  4ZWP A;  4IKR A;  2BWV A;  4R60 A;  3S6B A;  4FLJ A;  3D27 A;  2BWW A;  4HXX A;  1BN5 A;  5FCH A;  1YW8 A;  2GU5 A;  4U6J A;  1A16 A;  3FM3 A;  1C27 A;  4IPA A;  1C21 A;  5E2C A;  3OOO A;  3QOC A;  2GG7 A;  2GG3 A;  2BHA A;  3I7M A;  2BWX A;  2V3X A;  2BWY A;  5CDE A;  4B28 A;  4FLL A;  4U6Z A;  4EGE A;  2P98 A;  4S2T P;  4RGZ 1;  1BOA A;  4FUK A;  1C22 A;  3IL0 A;  2GG2 A;  2V6C A;  4FO7 A;  2B3L A;  4U73 A;  1Y1N A;  1M35 A;  3BIQ A;  1QZY A;  3CB6 A;  1XGS A;  2OKN A;  3FMR A;  4U71 A;  1WL9 A;  4IF7 A;  2BWU A;  1YW7 A;  2GU6 A;  3MAT A;  1C24 A;  1WN1 A;  5CLS A;  2ZSG A;  1XNZ A;  4FLK A;  4IDY A;  2BWT A;  3MX6 A;  1WL6 A;  1PV9 A;  3IG4 A;  4S01 A;  1QXZ A;  4OOK A;  4U69 A;  2BHD A;  1YJ3 A;  4U75 A;  1KQ9 A;  2IW2 A;  3PKC A;  2GGC A;  2BHB A;  5FCF A;  3PKD A;  1W7V A;  2BH3 A;  3IU8 A;  3L24 A;  5JI6 A;  4S2R P;  4RZZ A;  1W2M A;  4IEC A;  2NQ7 A;  1O0X A;  4IU6 A;  4U6W A;  2GG8 A;  1JAW A;  2OAZ A;  4JUQ A;  2Q92 A;  4U76 A;  3TB5 A; 
#chains in the Genus database with same CATH topology
 4IKS A;  2Q93 A;  4PV4 A;  1XGO A;  2B3H A;  2EVM A;  2GG9 A;  2V3Z A;  4IKT A;  4A6V A;  4Z7M A;  2GZ5 A;  4FKC A;  2GU7 A;  4IKU A;  1CHM A;  4MAT A;  3L7G A;  5JHU A;  1YVM A;  1WLR A;  4S00 A;  2P99 A;  3PKB A;  3PKE A;  3CTZ A;  2V3Y A;  1MAT A;  2EVO A;  1R58 A;  1QXY A;  2BB7 A;  2GG0 A;  2Q8K A;  4ZWU A;  5CDL A;  4PNC A;  2ADU A;  3BIP A;  3CB5 A;  5D6E A;  2MAT A;  2NQ6 A;  1WBQ A;  4U6E A;  5D6F A;  4KM3 A;  2G6P A;  3PKA A;  5CNX A;  3PN9 A;  2GG5 A;  4U1B A;  1B6A A;  3PEB A;  1R5H A;  2GGB A;  4U6C A;  3ROR A;  5E5B A;  1WY2 A;  3TAV A;  4U70 A;  1KP0 A;  2BN7 A;  5CE6 A;  2B3K A;  2GTX A;  1B59 A;  2Q94 A;  1XGN A;  2BHC A;  3FMQ A;  3IU9 A;  3Q6D A;  2EVC A;  2P9A A;  2HOW A;  4ZWO A;  4QR8 A;  4FLI A;  3OVK A;  5JFR A;  1C23 A;  2Q95 A;  1KQ0 A;  2EA2 A;  3O5V A;  1QXW A;  1N51 A;  3MR1 A;  1R5G A;  4FO8 A;  2DFI A;  4A6W A;  4RZY A;  4ZNG A;  1WKM A;  2Q96 A;  2BWS A;  2EA4 A;  2GA2 A;  1XGM A;  3BIT A;  1YW9 A;  2GU4 A;  5CDV A;  3IU7 A;  5CIK A;  3RVA A;  4ZWP A;  4IKR A;  2BWV A;  4R60 A;  3S6B A;  4FLJ A;  3D27 A;  2BWW A;  4HXX A;  1BN5 A;  5FCH A;  1YW8 A;  2GU5 A;  4U6J A;  1A16 A;  3FM3 A;  1C27 A;  4IPA A;  1C21 A;  5E2C A;  3OOO A;  3QOC A;  2GG7 A;  2GG3 A;  2BHA A;  3I7M A;  2BWX A;  2V3X A;  2BWY A;  5CDE A;  4B28 A;  4FLL A;  4U6Z A;  4EGE A;  2P98 A;  4S2T P;  4RGZ 1;  1BOA A;  4FUK A;  1C22 A;  3IL0 A;  2GG2 A;  2V6C A;  4FO7 A;  2B3L A;  4U73 A;  1Y1N A;  1M35 A;  3BIQ A;  1QZY A;  3CB6 A;  1XGS A;  2OKN A;  3FMR A;  4U71 A;  1WL9 A;  4IF7 A;  2BWU A;  1YW7 A;  2GU6 A;  3MAT A;  1C24 A;  1WN1 A;  5CLS A;  2ZSG A;  1XNZ A;  4FLK A;  4IDY A;  2BWT A;  3MX6 A;  1WL6 A;  1PV9 A;  3IG4 A;  4S01 A;  1QXZ A;  4OOK A;  4U69 A;  2BHD A;  1YJ3 A;  4U75 A;  1KQ9 A;  2IW2 A;  3PKC A;  2GGC A;  2BHB A;  5FCF A;  3PKD A;  1W7V A;  2BH3 A;  3IU8 A;  3L24 A;  5JI6 A;  4S2R P;  4RZZ A;  1W2M A;  4IEC A;  2NQ7 A;  1O0X A;  4IU6 A;  4U6W A;  2GG8 A;  1JAW A;  2OAZ A;  4JUQ A;  2Q92 A;  4U76 A;  3TB5 A; 
#chains in the Genus database with same CATH homology
 4IKS A;  2Q93 A;  4PV4 A;  1XGO A;  2B3H A;  2EVM A;  2GG9 A;  2V3Z A;  4IKT A;  4A6V A;  4Z7M A;  2GZ5 A;  4FKC A;  2GU7 A;  4IKU A;  1CHM A;  4MAT A;  3L7G A;  5JHU A;  1YVM A;  1WLR A;  4S00 A;  2P99 A;  3PKB A;  3PKE A;  3CTZ A;  2V3Y A;  1MAT A;  2EVO A;  1R58 A;  1QXY A;  2BB7 A;  2GG0 A;  2Q8K A;  4ZWU A;  5CDL A;  4PNC A;  2ADU A;  3BIP A;  3CB5 A;  5D6E A;  2MAT A;  2NQ6 A;  1WBQ A;  4U6E A;  5D6F A;  4KM3 A;  2G6P A;  3PKA A;  5CNX A;  3PN9 A;  2GG5 A;  4U1B A;  1B6A A;  3PEB A;  1R5H A;  2GGB A;  4U6C A;  3ROR A;  5E5B A;  1WY2 A;  3TAV A;  4U70 A;  1KP0 A;  2BN7 A;  5CE6 A;  2B3K A;  2GTX A;  1B59 A;  2Q94 A;  1XGN A;  2BHC A;  3FMQ A;  3IU9 A;  3Q6D A;  2EVC A;  2P9A A;  2HOW A;  4ZWO A;  4QR8 A;  4FLI A;  3OVK A;  5JFR A;  1C23 A;  2Q95 A;  1KQ0 A;  2EA2 A;  3O5V A;  1QXW A;  1N51 A;  3MR1 A;  1R5G A;  4FO8 A;  2DFI A;  4A6W A;  4RZY A;  4ZNG A;  1WKM A;  2Q96 A;  2BWS A;  2EA4 A;  2GA2 A;  1XGM A;  3BIT A;  1YW9 A;  2GU4 A;  5CDV A;  3IU7 A;  5CIK A;  3RVA A;  4ZWP A;  4IKR A;  2BWV A;  4R60 A;  3S6B A;  4FLJ A;  3D27 A;  2BWW A;  4HXX A;  1BN5 A;  5FCH A;  1YW8 A;  2GU5 A;  4U6J A;  1A16 A;  3FM3 A;  1C27 A;  4IPA A;  1C21 A;  5E2C A;  3OOO A;  3QOC A;  2GG7 A;  2GG3 A;  2BHA A;  3I7M A;  2BWX A;  2V3X A;  2BWY A;  5CDE A;  4B28 A;  4FLL A;  4U6Z A;  4EGE A;  2P98 A;  4S2T P;  4RGZ 1;  1BOA A;  4FUK A;  1C22 A;  3IL0 A;  2GG2 A;  2V6C A;  4FO7 A;  2B3L A;  4U73 A;  1Y1N A;  1M35 A;  3BIQ A;  1QZY A;  3CB6 A;  1XGS A;  2OKN A;  3FMR A;  4U71 A;  1WL9 A;  4IF7 A;  2BWU A;  1YW7 A;  2GU6 A;  3MAT A;  1C24 A;  1WN1 A;  5CLS A;  2ZSG A;  1XNZ A;  4FLK A;  4IDY A;  2BWT A;  3MX6 A;  1WL6 A;  1PV9 A;  3IG4 A;  4S01 A;  1QXZ A;  4OOK A;  4U69 A;  2BHD A;  1YJ3 A;  4U75 A;  1KQ9 A;  2IW2 A;  3PKC A;  2GGC A;  2BHB A;  5FCF A;  3PKD A;  1W7V A;  2BH3 A;  3IU8 A;  3L24 A;  5JI6 A;  4S2R P;  4RZZ A;  1W2M A;  4IEC A;  2NQ7 A;  1O0X A;  4IU6 A;  4U6W A;  2GG8 A;  1JAW A;  2OAZ A;  4JUQ A;  2Q92 A;  4U76 A;  3TB5 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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