4S01A

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp mutant d377n in complex with acrylate
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
RKIDPSRGATLGDGTPNDNDRIEIGPTQLAFSEWAAAGLQLPNLDRMREYRWKRLTQAIVDRGYGGLLMFDPLNIRYATDSTNMQLWNTHNPFRAVLLCADGYMVIWDYKNSPFLSKFNPLVREQRSGADLFYFDRGDKVDVQADVFANEVRVLMQDHAPGHTRLAVDKIMLHGLRALEAQGFEIMEGEEVTEKTRAIKGPDEILAMRCASHACETAVAEMEKFARAHVGDGKTSEDDIWAVLHAENIKRGGEWIETRLLASGPRTNPWFQECGPRITQKNEIIAFDTDLIGSYGICVDISRTWWIGDQKPRPDMVYAMQHAHEHIMTNMEMLKPGVMIPDLTANCHRLDDKFQAQKYGCLMHGVGLCNEWPLVAYPDKAVPGSYDYPLEPGMVLCVEAAVGEVGGDFSIKLEDQVLITEDGYENLTTYPFDAALMGLA
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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
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
source organism Silicibacter lacuscaerulensis iti-1157
molecule tags Lyase
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 4s01A01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4s01A02
4A6WA 2Q92A 4KM3A 4FKCA 4ZNGA 2BHAA 2G6PA 2BWWA 2GG8A 4FUKA 2Q95A 4FLJA 2BWVA 3PKEA 2BWTA 4B28A 4IKTA 3I7MA 2GGBA 1YVMA 4U6WA 3RORA 2HOWA 2BHDA 3BITA 3S6BA 4HXXA 4RZYA 3FMRA 2MATA 4RZZA 4FO7A 4FLLA 4IDYA 4U76A 2GZ5A 4U6EA 2GG3A 1XGMA 1C24A 4PV4A 2Q94A 2P98A 4FLIA 5JI6A 1XNZA 4S2TP 1BOAA 1WKMA 3MX6A 5JFRA 3TB5A 1KP0A 1QXZA 1QZYA 1YW7A 4PNCA 5CDVA 4Z7MA 2BB7A 2GU7A 5JHUA 1W7VA 1YW8A 1KQ9A 3OOOA 1C22A 2B3HA 4ZWOA 3BIPA 1YJ3A 2BWYA 2GG7A 2Q96A 1PV9A 5CLSA 5FCHA 3FM3A 1B6AA 1QXWA 3QOCA 1WN1A 2B3KA 5CIKA 1WBQA 1XGNA 2NQ7A 4U69A 5CE6A 3CB5A 1QXYA 4S00A 2BH3A 3IG4A 5CNXA 4IU6A 5D6EA 2Q93A 3OVKA 5D6FA 2GU5A 5E5BA 4R60A 1XGOA 1C23A 1WL9A 1O0XA 4S01A 4ZWUA 3IU7A 1WL6A 4U70A 2OAZA 4U6JA 4U6ZA 2BWXA 3IU9A 2EVOA 3L7GA 1M35A 4U73A 3CTZA 4FO8A 3L24A 2GTXA 2IW2A 3PKCA 2EVMA 4IKRA 2GU6A 1A16A 2P9AA 3IL0A 4EGEA 2GU4A 1MATA 4IKUA 4U1BA 2BWUA 2BWSA 1KQ0A 2V3XA 1XGSA 2BN7A 4U6CA 3O5VA 4JUQA 3CB6A 2BHBA 2GG9A 5E2CA 2EVCA 4OOKA 5CDEA 3IU8A 3BIQA 4IKSA 1C27A 3MATA 1C21A 3D27A 1W2MA 1YW9A 4IF7A 1WLRA 1R58A 1N51A 3Q6DA 2V3YA 3FMQA 4FLKA 4MATA 2P99A 4ZWPA 2BHCA 1R5HA 2GG2A 2GG0A 2V3ZA 3PKDA 2EA2A 5CDLA 3RVAA 4U71A 5FCFA 3PKBA 2GGCA 2Q8KA 2EA4A 2V6CA 4S2RP 3PKAA 2OKNA 3TAVA 3MR1A 2NQ6A 4U75A 1CHMA 1R5GA 1JAWA 2ZSGA 4RGZ1 2B3LA 1B59A 3PN9A 2GA2A 2GG5A 1Y1NA 4IPAA 4QR8A 4A6VA 2ADUA 2DFIA 4IECA 3PEBA 1BN5A 1WY2A
chains in the Genus database with same CATH superfamily
4A6WA 2Q92A 4KM3A 4FKCA 4ZNGA 2BHAA 2G6PA 2BWWA 2GG8A 4FUKA 2Q95A 4FLJA 2BWVA 3PKEA 2BWTA 4B28A 4IKTA 3I7MA 2GGBA 1YVMA 4U6WA 3RORA 2HOWA 2BHDA 3BITA 3S6BA 4HXXA 4RZYA 3FMRA 2MATA 4RZZA 4FO7A 4FLLA 4IDYA 4U76A 2GZ5A 4U6EA 2GG3A 1XGMA 1C24A 4PV4A 2Q94A 2P98A 4FLIA 5JI6A 1XNZA 4S2TP 1BOAA 1WKMA 3MX6A 5JFRA 3TB5A 1KP0A 1QXZA 1QZYA 1YW7A 4PNCA 5CDVA 4Z7MA 2BB7A 2GU7A 5JHUA 1W7VA 1YW8A 1KQ9A 3OOOA 1C22A 2B3HA 4ZWOA 3BIPA 1YJ3A 2BWYA 2GG7A 2Q96A 1PV9A 5CLSA 5FCHA 3FM3A 1B6AA 1QXWA 3QOCA 1WN1A 2B3KA 5CIKA 1WBQA 1XGNA 2NQ7A 4U69A 5CE6A 3CB5A 1QXYA 4S00A 2BH3A 3IG4A 5CNXA 4IU6A 5D6EA 2Q93A 3OVKA 5D6FA 2GU5A 5E5BA 4R60A 1XGOA 1C23A 1WL9A 1O0XA 4S01A 4ZWUA 3IU7A 1WL6A 4U70A 2OAZA 4U6JA 4U6ZA 2BWXA 3IU9A 2EVOA 3L7GA 1M35A 4U73A 3CTZA 4FO8A 3L24A 2GTXA 2IW2A 3PKCA 2EVMA 4IKRA 2GU6A 1A16A 2P9AA 3IL0A 4EGEA 2GU4A 1MATA 4IKUA 4U1BA 2BWUA 2BWSA 1KQ0A 2V3XA 1XGSA 2BN7A 4U6CA 3O5VA 4JUQA 3CB6A 2BHBA 2GG9A 5E2CA 2EVCA 4OOKA 5CDEA 3IU8A 3BIQA 4IKSA 1C27A 3MATA 1C21A 3D27A 1W2MA 1YW9A 4IF7A 1WLRA 1R58A 1N51A 3Q6DA 2V3YA 3FMQA 4FLKA 4MATA 2P99A 4ZWPA 2BHCA 1R5HA 2GG2A 2GG0A 2V3ZA 3PKDA 2EA2A 5CDLA 3RVAA 4U71A 5FCFA 3PKBA 2GGCA 2Q8KA 2EA4A 2V6CA 4S2RP 3PKAA 2OKNA 3TAVA 3MR1A 2NQ6A 4U75A 1CHMA 1R5GA 1JAWA 2ZSGA 4RGZ1 2B3LA 1B59A 3PN9A 2GA2A 2GG5A 1Y1NA 4IPAA 4QR8A 4A6VA 2ADUA 2DFIA 4IECA 3PEBA 1BN5A 1WY2A
chains in the Genus database with same CATH topology
4A6WA 2Q92A 4KM3A 4FKCA 4ZNGA 2BHAA 2G6PA 2BWWA 2GG8A 4FUKA 2Q95A 4FLJA 2BWVA 3PKEA 2BWTA 4B28A 4IKTA 3I7MA 2GGBA 1YVMA 4U6WA 3RORA 2HOWA 2BHDA 3BITA 3S6BA 4HXXA 4RZYA 3FMRA 2MATA 4RZZA 4FO7A 4FLLA 4IDYA 4U76A 2GZ5A 4U6EA 2GG3A 1XGMA 1C24A 4PV4A 2Q94A 2P98A 4FLIA 5JI6A 1XNZA 4S2TP 1BOAA 1WKMA 3MX6A 5JFRA 3TB5A 1KP0A 1QXZA 1QZYA 1YW7A 4PNCA 5CDVA 4Z7MA 2BB7A 2GU7A 5JHUA 1W7VA 1YW8A 1KQ9A 3OOOA 1C22A 2B3HA 4ZWOA 3BIPA 1YJ3A 2BWYA 2GG7A 2Q96A 1PV9A 5CLSA 5FCHA 3FM3A 1B6AA 1QXWA 3QOCA 1WN1A 2B3KA 5CIKA 1WBQA 1XGNA 2NQ7A 4U69A 5CE6A 3CB5A 1QXYA 4S00A 2BH3A 3IG4A 5CNXA 4IU6A 5D6EA 2Q93A 3OVKA 5D6FA 2GU5A 5E5BA 4R60A 1XGOA 1C23A 1WL9A 1O0XA 4S01A 4ZWUA 3IU7A 1WL6A 4U70A 2OAZA 4U6JA 4U6ZA 2BWXA 3IU9A 2EVOA 3L7GA 1M35A 4U73A 3CTZA 4FO8A 3L24A 2GTXA 2IW2A 3PKCA 2EVMA 4IKRA 2GU6A 1A16A 2P9AA 3IL0A 4EGEA 2GU4A 1MATA 4IKUA 4U1BA 2BWUA 2BWSA 1KQ0A 2V3XA 1XGSA 2BN7A 4U6CA 3O5VA 4JUQA 3CB6A 2BHBA 2GG9A 5E2CA 2EVCA 4OOKA 5CDEA 3IU8A 3BIQA 4IKSA 1C27A 3MATA 1C21A 3D27A 1W2MA 1YW9A 4IF7A 1WLRA 1R58A 1N51A 3Q6DA 2V3YA 3FMQA 4FLKA 4MATA 2P99A 4ZWPA 2BHCA 1R5HA 2GG2A 2GG0A 2V3ZA 3PKDA 2EA2A 5CDLA 3RVAA 4U71A 5FCFA 3PKBA 2GGCA 2Q8KA 2EA4A 2V6CA 4S2RP 3PKAA 2OKNA 3TAVA 3MR1A 2NQ6A 4U75A 1CHMA 1R5GA 1JAWA 2ZSGA 4RGZ1 2B3LA 1B59A 3PN9A 2GA2A 2GG5A 1Y1NA 4IPAA 4QR8A 4A6VA 2ADUA 2DFIA 4IECA 3PEBA 1BN5A 1WY2A
chains in the Genus database with same CATH homology


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