4YIZ | Genus

Total Genus 102

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	102
sequence length	399
structure length	392
Chain Sequence	SGNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSNPSVTPPTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTADEQNEC

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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The Resolver thinks Pdb

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Time for openFile(/file/5d00d73482694ae9a44e0bce/pdb.gz): 1724 ms

reading 392 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

392 atoms created

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

Time for creating model: 35 ms

Adding embedded #jmolscript: select ({0:391});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

molecule tags	Immune system
source organism	Toxoplasma gondii me49
publication title	An Extended Surface Loop on Toxoplasma gondii Apical Membrane Antigen 1 (AMA1) Governs Ligand Binding Selectivity. pubmed doi rcsb
molecule keywords	Apical membrane antigen AMA1
total genus	102
structure length	392
sequence length	399
chains with identical sequence	C, E
ec nomenclature
pdb deposition date	2015-03-02

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02430	AMA-1	Apical membrane antigen 1

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

cath code	Class	Architecture	Topology	Homology	Domain
2.10.70.70	Mainly Beta	Ribbon	Complement Module; domain 1	Complement Module; domain 1	4yizA03
3.50.4.30	Alpha Beta	3-Layer(bba) Sandwich	Hepatocyte Growth Factor	Hepatocyte Growth Factor	4yizA01

2X2ZA 4YIZA 3ZLDA 3ZLEA 4YIVA 2Y8RA 2Y8TA 4APLA 2Y8SA
chains in the Genus database with same CATH superfamily

3HN4A 3ZD1A 1GPZA 2ERJA 1OK2A 1ZJKA 2RLQA 4PO7A 3K3TA 4MSLA 5I0QB 3NJAA 1Z92B 3OXUD 3ZD2A 4WJG2 1E8BA 3ZRZA 1QUBA 1CKLA 2JRAA 4AYEA 2Z8WA 4R1CA 1RLHA 2G7IA 2UWNA 2QJ4A 2XQWC 2YIOA 4J38B 2JGWA 3TVJA 3FGTA 1I8NA 1OK9A 4C16A 3O8EB 2LL3A 1E5GA 3SRJA 1W81A 1HCCA 5EODA 1GKGA 5FO8C 3HMTA 1GP9A 4APMA 5HYUB 4KKDA 3FGRA 5CSQA 3SW0X 2RKYA 2A55A 5JPMG 4R1BA 4LOSA 3SRIA 4K12A 3HMRA 4Z0EA 1QO6A 2YILA 3INBC 5DN5A 2K13X 4R19A 1YXEA 4UV6A 2KRIA 3T5OA 4F4OC 5CS9A 2CKUA 2J8JA 4Z09A 2J8LA 2MCZA 5HYPA 1OK3A 3MKPA 2KL5A 2WIIC 4ONTD 4B2RA 4BWCA 5HZPB 3KZJA 4N7EA 4UAOA 1MD7A 1OK1A 3CI0J 4AYDA 1W8KA 1OJYA 3MQLA 1HKYA 1O9AA 2XRBA 3VWOA 2IZ4A 3OEDC 1GMOA 4DURA 3KXVA 3NFPI 4APLA 5CS1A 3WSYA 2HGFA 2XWBF 5I25A 4FXGG 1UOTP 5DN4A 1Z40A 2EHFA 3ZLEA 2YRAA 2QY0A 2W81A 1NWVA 2W80A 2XRDA 3EJHA 2O39C 3GOVA 4A5WB 4IUAA 4Z0DA 5COEA 5CT3A 2XWJI 2Y8RA 2ZYCA 2I2LA 1FBRA 1H2QP 3SP8A 4Z0FA 2YIPA 5CP9A 1PPQA 1H04P 3L89M 2CG7A 1ELVA 4YIVA 2MCYA 2CG6A 1TPGA 3F6KA 2Y8TA 5CS5A 1HFIA 3OP8A 2QJ2A 2Q8BA 4A5TS 1U5MA 1NK1A 5CT1A 1E88A 3GXEA 1GMNA 2JGXA 2Y8SA 3ZLDA 1BHTA 5EOKA 4YIZA 2KMSA 3ZWZA 3IU3I 1LY2A 1QGBA 2Q8AA 1G4GA 1SRZA 1TPMA 1C1ZA 1MD8A 1OJWA 2X2ZA 3IX0A 1H2PP 1H03P 3RJ3D 4B2SA 1Q3XA 3ERBA 2RKZA 2V8EA 2YBYA 3M7PA 1OJVA 3R62A 4IGDA 4JHSA 4LOTA 4PZ5A 2F83A 1VVCA 5CT2A 4AYIA 4DJZA 2EC3A 4AYMA 1VVDA 1HFHA 2IZ3A 2RL0A 4CSYA 4ZH1D 5HYTB 1SS2A 1TPNA 4YNXA 2LL4M 2LOJA 3HMSA 2B5ID 4MUCA 2RLPA 2BZMA 1GHQB 3CALA 1G4FA 2Z8VA 1GKNA 4R1AA 5CS3A 3WSXA
chains in the Genus database with same CATH topology

3HN4A 4PO7A 4MSLA 3NJAA 2Z8WA 4R1CA 2QJ4A 2YIOA 3FGTA 1I8NA 2LL3A 3SRJA 1W81A 5EODA 3HMTA 1GP9A 4APMA 5CSQA 3FGRA 4R1BA 3SRIA 3HMRA 4Z0EA 2YILA 2K13X 4R19A 1YXEA 4UV6A 5CS9A 2J8JA 4Z09A 2J8LA 3MKPA 2KL5A 4BWCA 4N7EA 4UAOA 1W8KA 1HKYA 4DURA 1GMOA 4APLA 5CS1A 3WSYA 2HGFA 5I25A 1Z40A 3ZLEA 4IUAA 4Z0DA 5COEA 5CT3A 2Y8RA 2I2LA 4Z0FA 3SP8A 2YIPA 5CP9A 4YIVA 3F6KA 2Y8TA 5CS5A 2QJ2A 2Q8BA 4A5TS 5CT1A 1GMNA 2Y8SA 3ZLDA 1BHTA 5EOKA 4YIZA 3ZWZA 2Q8AA 2X2ZA 2F83A 5CT2A 1NK1A 2LL4M 3HMSA 2Z8VA 4R1AA 5CS3A 3WSXA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2X2Z A;  4YIZ A;  3ZLD A;  3ZLE A;  4YIV A;  2Y8R A;  2Y8T A;  4APL A;  2Y8S A; 
#chains in the Genus database with same CATH topology
 3HN4 A;  3ZD1 A;  1GPZ A;  2ERJ A;  1OK2 A;  1ZJK A;  2RLQ A;  4PO7 A;  3K3T A;  4MSL A;  5I0Q B;  3NJA A;  1Z92 B;  3OXU D;  3ZD2 A;  4WJG 2;  1E8B A;  3ZRZ A;  1QUB A;  1CKL A;  2JRA A;  4AYE A;  2Z8W A;  4R1C A;  1RLH A;  2G7I A;  2UWN A;  2QJ4 A;  2XQW C;  2YIO A;  4J38 B;  2JGW A;  3TVJ A;  3FGT A;  1I8N A;  1OK9 A;  4C16 A;  3O8E B;  2LL3 A;  1E5G A;  3SRJ A;  1W81 A;  1HCC A;  5EOD A;  1GKG A;  5FO8 C;  3HMT A;  1GP9 A;  4APM A;  5HYU B;  4KKD A;  3FGR A;  5CSQ A;  3SW0 X;  2RKY A;  2A55 A;  5JPM G;  4R1B A;  4LOS A;  3SRI A;  4K12 A;  3HMR A;  4Z0E A;  1QO6 A;  2YIL A;  3INB C;  5DN5 A;  2K13 X;  4R19 A;  1YXE A;  4UV6 A;  2KRI A;  3T5O A;  4F4O C;  5CS9 A;  2CKU A;  2J8J A;  4Z09 A;  2J8L A;  2MCZ A;  5HYP A;  1OK3 A;  3MKP A;  2KL5 A;  2WII C;  4ONT D;  4B2R A;  4BWC A;  5HZP B;  3KZJ A;  4N7E A;  4UAO A;  1MD7 A;  1OK1 A;  3CI0 J;  4AYD A;  1W8K A;  1OJY A;  3MQL A;  1HKY A;  1O9A A;  2XRB A;  3VWO A;  2IZ4 A;  3OED C;  1GMO A;  4DUR A;  3KXV A;  3NFP I;  4APL A;  5CS1 A;  3WSY A;  2HGF A;  2XWB F;  5I25 A;  4FXG G;  1UOT P;  5DN4 A;  1Z40 A;  2EHF A;  3ZLE A;  2YRA A;  2QY0 A;  2W81 A;  1NWV A;  2W80 A;  2XRD A;  3EJH A;  2O39 C;  3GOV A;  4A5W B;  4IUA A;  4Z0D A;  5COE A;  5CT3 A;  2XWJ I;  2Y8R A;  2ZYC A;  2I2L A;  1FBR A;  1H2Q P;  3SP8 A;  4Z0F A;  2YIP A;  5CP9 A;  1PPQ A;  1H04 P;  3L89 M;  2CG7 A;  1ELV A;  4YIV A;  2MCY A;  2CG6 A;  1TPG A;  3F6K A;  2Y8T A;  5CS5 A;  1HFI A;  3OP8 A;  2QJ2 A;  2Q8B A;  4A5T S;  1U5M A;  1NK1 A;  5CT1 A;  1E88 A;  3GXE A;  1GMN A;  2JGX A;  2Y8S A;  3ZLD A;  1BHT A;  5EOK A;  4YIZ A;  2KMS A;  3ZWZ A;  3IU3 I;  1LY2 A;  1QGB A;  2Q8A A;  1G4G A;  1SRZ A;  1TPM A;  1C1Z A;  1MD8 A;  1OJW A;  2X2Z A;  3IX0 A;  1H2P P;  1H03 P;  3RJ3 D;  4B2S A;  1Q3X A;  3ERB A;  2RKZ A;  2V8E A;  2YBY A;  3M7P A;  1OJV A;  3R62 A;  4IGD A;  4JHS A;  4LOT A;  4PZ5 A;  2F83 A;  1VVC A;  5CT2 A;  4AYI A;  4DJZ A;  2EC3 A;  4AYM A;  1VVD A;  1HFH A;  2IZ3 A;  2RL0 A;  4CSY A;  4ZH1 D;  5HYT B;  1SS2 A;  1TPN A;  4YNX A;  2LL4 M;  2LOJ A;  3HMS A;  2B5I D;  4MUC A;  2RLP A;  2BZM A;  1GHQ B;  3CAL A;  1G4F A;  2Z8V A;  1GKN A;  4R1A A;  5CS3 A;  3WSX A; 
#chains in the Genus database with same CATH homology
 3HN4 A;  4PO7 A;  4MSL A;  3NJA A;  2Z8W A;  4R1C A;  2QJ4 A;  2YIO A;  3FGT A;  1I8N A;  2LL3 A;  3SRJ A;  1W81 A;  5EOD A;  3HMT A;  1GP9 A;  4APM A;  5CSQ A;  3FGR A;  4R1B A;  3SRI A;  3HMR A;  4Z0E A;  2YIL A;  2K13 X;  4R19 A;  1YXE A;  4UV6 A;  5CS9 A;  2J8J A;  4Z09 A;  2J8L A;  3MKP A;  2KL5 A;  4BWC A;  4N7E A;  4UAO A;  1W8K A;  1HKY A;  4DUR A;  1GMO A;  4APL A;  5CS1 A;  3WSY A;  2HGF A;  5I25 A;  1Z40 A;  3ZLE A;  4IUA A;  4Z0D A;  5COE A;  5CT3 A;  2Y8R A;  2I2L A;  4Z0F A;  3SP8 A;  2YIP A;  5CP9 A;  4YIV A;  3F6K A;  2Y8T A;  5CS5 A;  2QJ2 A;  2Q8B A;  4A5T S;  5CT1 A;  1GMN A;  2Y8S A;  3ZLD A;  1BHT A;  5EOK A;  4YIZ A;  3ZWZ A;  2Q8A A;  2X2Z A;  2F83 A;  5CT2 A;  1NK1 A;  2LL4 M;  3HMS A;  2Z8V A;  4R1A A;  5CS3 A;  3WSX 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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#similar chains in the pdb database (?% sequence similarity)
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4YIZA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations