4S00A

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp mutant y366a 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
RKIDPSRGATLGDGTPNDNDRIEIGPTQLAFSEWAAAGLQLPNLDRMREYRWKRLTQAIVDRGYGGLLMFDPLNIRYATDSTNMQLWNTHNPFRAVLLCADGYMVIWDYKNSPFLSKFNPLVREQRSGADLFYFDRGDKVDVQADVFANEVRVLMQDHAPGHTRLAVDKIMLHGLRALEAQGFEIMEGEEVTEKTRAIKGPDEILAMRCASHACETAVAEMEKFARAHVGDGKTSEDDIWAVLHAENIKRGGEWIETRLLASGPRTNPWFQECGPRITQKNEIIAFDTDLIGSYGICVDISRTWWIGDQKPRPDMVYAMQHAHEHIMTNMEMLKPGVMIPDLTANCHRLDDKFQAQKAGCLMHGVGLCDEWPLVAYPDKAVPGSYDYPLEPGMVLCVEAAVGEVGGDFSIKLEDQVLITEDGYENLTTYPFDAALMGLA
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.

molecule tags Lyase
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
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 4s00A01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4s00A02
1B6AA 3IL0A 4RZYA 1YJ3A 3OVKA 4U71A 4IECA 4A6VA 1WL6A 5D6FA 1BOAA 4ZWPA 4IKRA 3PKAA 4U73A 1C21A 2BB7A 4IU6A 2EVMA 1JAWA 1WN1A 3PN9A 1XGSA 2GG7A 3IU9A 2GU5A 4A6WA 3TB5A 4S01A 4FO8A 2EA4A 4FKCA 1C24A 4S2TP 4FO7A 1YW9A 1XGOA 2Q94A 2Q8KA 1M35A 2GU4A 4RGZ1 3Q6DA 4B28A 3CB5A 4ZNGA 2GG3A 2P9AA 1KQ0A 2GZ5A 2BWYA 1XGMA 1QXWA 4U69A 2Q95A 1O0XA 4FUKA 4OOKA 1PV9A 3CTZA 5CNXA 1YVMA 2V3XA 3RVAA 3BIQA 2HOWA 2GG0A 2GGBA 3RORA 4FLKA 3MX6A 1N51A 1WY2A 4QR8A 4HXXA 1KQ9A 1XNZA 2OAZA 2B3HA 1A16A 1Y1NA 2BHDA 2NQ7A 3OOOA 3FMQA 5E5BA 4EGEA 3FMRA 3PKEA 4FLLA 2GU6A 1WBQA 3O5VA 2BWWA 1YW7A 4S2RP 2GTXA 4U75A 2BHAA 2BH3A 5CLSA 4IKTA 2GG9A 4FLIA 1W2MA 4IDYA 3QOCA 2GG5A 2GU7A 1MATA 1BN5A 2B3LA 2GA2A 5D6EA 2BWTA 1C22A 2BWVA 1YW8A 2EVOA 3L7GA 2EVCA 4U6JA 1WLRA 3MATA 2OKNA 1C23A 2Q93A 4U1BA 2P99A 3FM3A 2ADUA 3BITA 1R5GA 4ZWUA 3IU7A 5CE6A 3IG4A 5E2CA 2BWSA 1R58A 1XGNA 4FLJA 4Z7MA 3IU8A 2BWUA 5CDLA 1R5HA 1QZYA 3TAVA 2IW2A 4U6CA 3D27A 4RZZA 2DFIA 4MATA 1QXYA 3MR1A 3PEBA 4IKSA 3I7MA 2BN7A 4JUQA 1B59A 4IKUA 4U6WA 2BHCA 1CHMA 3BIPA 2GGCA 4PNCA 2NQ6A 5JI6A 1WL9A 4IPAA 3CB6A 5CIKA 5CDEA 5FCHA 2B3KA 1W7VA 4R60A 1QXZA 4S00A 1WKMA 4ZWOA 2EA2A 3PKCA 3PKBA 4U70A 2GG8A 4KM3A 2GG2A 4U76A 2V3YA 2BHBA 2MATA 4U6EA 2V3ZA 5CDVA 2Q96A 1KP0A 4IF7A 5JFRA 2G6PA 2ZSGA 5JHUA 3S6BA 4PV4A 2P98A 4U6ZA 2BWXA 5FCFA 2V6CA 2Q92A 3PKDA 1C27A 3L24A
chains in the Genus database with same CATH superfamily
1B6AA 3IL0A 4RZYA 1YJ3A 3OVKA 4U71A 4IECA 4A6VA 1WL6A 5D6FA 1BOAA 4ZWPA 4IKRA 3PKAA 4U73A 1C21A 2BB7A 4IU6A 2EVMA 1JAWA 1WN1A 3PN9A 1XGSA 2GG7A 3IU9A 2GU5A 4A6WA 3TB5A 4S01A 4FO8A 2EA4A 4FKCA 1C24A 4S2TP 4FO7A 1YW9A 1XGOA 2Q94A 2Q8KA 1M35A 2GU4A 4RGZ1 3Q6DA 4B28A 3CB5A 4ZNGA 2GG3A 2P9AA 1KQ0A 2GZ5A 2BWYA 1XGMA 1QXWA 4U69A 2Q95A 1O0XA 4FUKA 4OOKA 1PV9A 3CTZA 5CNXA 1YVMA 2V3XA 3RVAA 3BIQA 2HOWA 2GG0A 2GGBA 3RORA 4FLKA 3MX6A 1N51A 1WY2A 4QR8A 4HXXA 1KQ9A 1XNZA 2OAZA 2B3HA 1A16A 1Y1NA 2BHDA 2NQ7A 3OOOA 3FMQA 5E5BA 4EGEA 3FMRA 3PKEA 4FLLA 2GU6A 1WBQA 3O5VA 2BWWA 1YW7A 4S2RP 2GTXA 4U75A 2BHAA 2BH3A 5CLSA 4IKTA 2GG9A 4FLIA 1W2MA 4IDYA 3QOCA 2GG5A 2GU7A 1MATA 1BN5A 2B3LA 2GA2A 5D6EA 2BWTA 1C22A 2BWVA 1YW8A 2EVOA 3L7GA 2EVCA 4U6JA 1WLRA 3MATA 2OKNA 1C23A 2Q93A 4U1BA 2P99A 3FM3A 2ADUA 3BITA 1R5GA 4ZWUA 3IU7A 5CE6A 3IG4A 5E2CA 2BWSA 1R58A 1XGNA 4FLJA 4Z7MA 3IU8A 2BWUA 5CDLA 1R5HA 1QZYA 3TAVA 2IW2A 4U6CA 3D27A 4RZZA 2DFIA 4MATA 1QXYA 3MR1A 3PEBA 4IKSA 3I7MA 2BN7A 4JUQA 1B59A 4IKUA 4U6WA 2BHCA 1CHMA 3BIPA 2GGCA 4PNCA 2NQ6A 5JI6A 1WL9A 4IPAA 3CB6A 5CIKA 5CDEA 5FCHA 2B3KA 1W7VA 4R60A 1QXZA 4S00A 1WKMA 4ZWOA 2EA2A 3PKCA 3PKBA 4U70A 2GG8A 4KM3A 2GG2A 4U76A 2V3YA 2BHBA 2MATA 4U6EA 2V3ZA 5CDVA 2Q96A 1KP0A 4IF7A 5JFRA 2G6PA 2ZSGA 5JHUA 3S6BA 4PV4A 2P98A 4U6ZA 2BWXA 5FCFA 2V6CA 2Q92A 3PKDA 1C27A 3L24A
chains in the Genus database with same CATH topology
1B6AA 3IL0A 4RZYA 1YJ3A 3OVKA 4U71A 4IECA 4A6VA 1WL6A 5D6FA 1BOAA 4ZWPA 4IKRA 3PKAA 4U73A 1C21A 2BB7A 4IU6A 2EVMA 1JAWA 1WN1A 3PN9A 1XGSA 2GG7A 3IU9A 2GU5A 4A6WA 3TB5A 4S01A 4FO8A 2EA4A 4FKCA 1C24A 4S2TP 4FO7A 1YW9A 1XGOA 2Q94A 2Q8KA 1M35A 2GU4A 4RGZ1 3Q6DA 4B28A 3CB5A 4ZNGA 2GG3A 2P9AA 1KQ0A 2GZ5A 2BWYA 1XGMA 1QXWA 4U69A 2Q95A 1O0XA 4FUKA 4OOKA 1PV9A 3CTZA 5CNXA 1YVMA 2V3XA 3RVAA 3BIQA 2HOWA 2GG0A 2GGBA 3RORA 4FLKA 3MX6A 1N51A 1WY2A 4QR8A 4HXXA 1KQ9A 1XNZA 2OAZA 2B3HA 1A16A 1Y1NA 2BHDA 2NQ7A 3OOOA 3FMQA 5E5BA 4EGEA 3FMRA 3PKEA 4FLLA 2GU6A 1WBQA 3O5VA 2BWWA 1YW7A 4S2RP 2GTXA 4U75A 2BHAA 2BH3A 5CLSA 4IKTA 2GG9A 4FLIA 1W2MA 4IDYA 3QOCA 2GG5A 2GU7A 1MATA 1BN5A 2B3LA 2GA2A 5D6EA 2BWTA 1C22A 2BWVA 1YW8A 2EVOA 3L7GA 2EVCA 4U6JA 1WLRA 3MATA 2OKNA 1C23A 2Q93A 4U1BA 2P99A 3FM3A 2ADUA 3BITA 1R5GA 4ZWUA 3IU7A 5CE6A 3IG4A 5E2CA 2BWSA 1R58A 1XGNA 4FLJA 4Z7MA 3IU8A 2BWUA 5CDLA 1R5HA 1QZYA 3TAVA 2IW2A 4U6CA 3D27A 4RZZA 2DFIA 4MATA 1QXYA 3MR1A 3PEBA 4IKSA 3I7MA 2BN7A 4JUQA 1B59A 4IKUA 4U6WA 2BHCA 1CHMA 3BIPA 2GGCA 4PNCA 2NQ6A 5JI6A 1WL9A 4IPAA 3CB6A 5CIKA 5CDEA 5FCHA 2B3KA 1W7VA 4R60A 1QXZA 4S00A 1WKMA 4ZWOA 2EA2A 3PKCA 3PKBA 4U70A 2GG8A 4KM3A 2GG2A 4U76A 2V3YA 2BHBA 2MATA 4U6EA 2V3ZA 5CDVA 2Q96A 1KP0A 4IF7A 5JFRA 2G6PA 2ZSGA 5JHUA 3S6BA 4PV4A 2P98A 4U6ZA 2BWXA 5FCFA 2V6CA 2Q92A 3PKDA 1C27A 3L24A
chains in the Genus database with same CATH homology


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