5CDE | Genus

Total Genus 133

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	133
sequence length	398
structure length	398
Chain Sequence	STQIGGMSLDQARTQLAPWTQRAAPIGADEYQQRIERARVLMRAQGVDALLIGAGTSLRYFSGVPWGASERLVALLLTTEGDPVLICPAFEEGSLDAVLQLPVRKRLWEEHEDPYALVVQAMDEQHAHALALDPGIAFAVHTGLRAHLGTAIRDAGAIIDGCRMCKSPAELALMQQACDMTLLVQRLAAGIAHEGIGTDQLVRFIDEAHRALGADNGSTFCIVQFGHATAFPHGIPGVQHLRAGELVLIDTGCTVQGYHSDITRTWIYGTPSDAQQRIWELELAAQAAAFAAVRPGVACEAVDQAARAVLQAAGLGPDYRLPGLPHRTGHGCGLAIHEAPYLVRGNRQPLQPGMCASNEPMIVVPGAFGVALEDHFYVTDTGAQWFTPPSVAIDQPFA

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

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Viewer cachePut cache://localLOAD_/file/5d0155923e61c76144eed04b/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d0155923e61c76144eed04b/pdb.gz): 1165 ms

reading 398 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

398 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:397});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Hydrolase
source organism	Xanthomonas campestris
publication title	R372A mutant of Xaa-Pro dipeptidase from Xanthomonas campestris at 1.85 Angstrom resolution rcsb
molecule keywords	Proline dipeptidase
total genus	133
structure length	398
sequence length	398
chains with identical sequence	B
ec nomenclature
pdb deposition date	2015-07-03

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00557	Peptidase_M24	Metallopeptidase family M24
A	PF01321	Creatinase_N	Creatinase/Prolidase N-terminal domain

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase; Chain A, domain 1	Creatinase/prolidase N-terminal domain	5cdeA01
3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	5cdeA02

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations