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


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