4JHS | Genus

Total Genus 24

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	24
sequence length	142
structure length	142
Chain Sequence	KCPFPSRPDNGFVNYPAKPTLYYKDKATFGCHDGYSLDGPEEIECTKLGNWSAMPSCKASCKVPVKKATVVYQGERVKIQEKFKNGMLHGDKVSFFCKNKEKKCSYTEDAQCIDGTIEVPKCFKEHSSLAFWKTDASDVKPC

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/5d005dce7ed72cb3dc388342/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d005dce7ed72cb3dc388342/pdb.gz): 1175 ms

reading 142 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

142 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:141});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	Signaling protein
source organism	Homo sapiens
publication title	Crystal structure of a C-terminal two domain fragment of human beta-2-glycoprotein 1 rcsb
molecule keywords	Beta-2-glycoprotein 1
total genus	24
structure length	142
sequence length	142
ec nomenclature
pdb deposition date	2013-03-05

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00084	Sushi	Sushi repeat (SCR repeat)
A	PF09014	Sushi_2	Beta-2-glycoprotein-1 fifth domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.10.70.10	Mainly Beta	Ribbon	Complement Module; domain 1	Complement Module, domain 1	4jhsA01
2.10.70.10	Mainly Beta	Ribbon	Complement Module; domain 1	Complement Module, domain 1	4jhsA02

1FBRA 1HFIA 3RJ3D 4AYIA 1UOTP 4J38B 1GKGA 1Z92B 4AYDA 5JPMG 2UWNA 1OK9A 2W81A 3R62A 1E5GA 3IU3I 1OJYA 5HZPB 2EHFA 1HCCA 1VVDA 4PZ5A 5HYUB 2B5ID 4B2SA 2W80A 2RKZA 1H03P 1E8BA 1OJWA 3OP8A 4MUCA 1O9AA 1H2QP 2JGXA 3SW0X 1NWVA 2RLQA 1C1ZA 3MQLA 1SS2A 3OEDC 1G4FA 2CG6A 2IZ4A 4AYMA 2CG7A 2MCYA 3TVJA 2ERJA 3GXEA 1U5MA 1HFHA 2XRBA 3ERBA 5FO8C 1OK1A 2YRAA 2EC3A 1TPNA 5HYTB 3O8EB 3INBC 1OJVA 1LY2A 3T5OA 2O39C 1SRZA 2KMSA 5I0QB 2JGWA 3OXUD 4CSYA 4KKDA 1G4GA 3NFPI 1TPGA 1ZJKA 4C16A 3EJHA 2RKYA 1OK3A 4K12A 1TPMA 1H2PP 2CKUA 1GKNA 3KZJA 3KXVA 3ZD1A 1VVCA 2A55A 4LOTA 4LOSA 1QUBA 2JRAA 2IZ3A 1H04P 1QO6A 1MD8A 1PPQA 3IX0A 3M7PA 1GPZA 2YBYA 3ZD2A 2WIIC 4A5WB 1MD7A 4ONTD 2LOJA 2QY0A 2RLPA 3CALA 4B2RA 4YNXA 1OK2A 1CKLA 3L89M 4AYEA 4FXGG 2XQWC 1GHQB 4DJZA 2V8EA 2MCZA 2XWBF 2KRIA 2XRDA 5HYPA 4ZH1D 2G7IA 1QGBA 3GOVA 4WJG2 1E88A 2XWJI 2RL0A 1ELVA 4IGDA 1Q3XA 3ZRZA 2BZMA 4JHSA 4F4OC
chains in the Genus database with same CATH superfamily

1FBRA 1HFIA 3RJ3D 4AYIA 1UOTP 4J38B 1GKGA 1Z92B 4AYDA 5JPMG 2UWNA 1OK9A 2W81A 3R62A 1E5GA 3IU3I 1OJYA 5HZPB 2EHFA 3ZLDA 1HCCA 1VVDA 4PZ5A 5HYUB 2B5ID 4B2SA 2W80A 4MSLA 2RKZA 2X2ZA 1H03P 1E8BA 3NJAA 1OJWA 3OP8A 4MUCA 1O9AA 1H2QP 2JGXA 3SW0X 1NWVA 2RLQA 2Y8RA 1C1ZA 3MQLA 1SS2A 3OEDC 1G4FA 2CG6A 2IZ4A 4APLA 4AYMA 2CG7A 2MCYA 3TVJA 2ERJA 3GXEA 2ZYCA 1U5MA 1HFHA 2XRBA 3ERBA 5FO8C 1OK1A 2YRAA 2EC3A 1TPNA 5HYTB 3O8EB 3INBC 1OJVA 1LY2A 3WSXA 3T5OA 2O39C 1SRZA 2KMSA 5I0QB 2JGWA 3OXUD 4CSYA 4KKDA 5DN4A 1G4GA 3NFPI 4PO7A 1TPGA 1ZJKA 4C16A 3EJHA 2RKYA 1OK3A 4K12A 1TPMA 1H2PP 4N7EA 2CKUA 1GKNA 3KZJA 3KXVA 3ZD1A 1RLHA 1VVCA 2A55A 4LOTA 4LOSA 1QUBA 3CI0J 2JRAA 3VWOA 2IZ3A 1H04P 1QO6A 1MD8A 1PPQA 3FGTA 2Y8SA 5DN5A 3IX0A 3M7PA 1GPZA 2YBYA 3ZD2A 2WIIC 4A5WB 1MD7A 4ONTD 2LOJA 2QY0A 2RLPA 3CALA 2I2LA 4B2RA 4YNXA 1OK2A 1CKLA 3L89M 4AYEA 4FXGG 2XQWC 4BWCA 1GHQB 4YIZA 4DJZA 2V8EA 2MCZA 2XWBF 2KRIA 3WSYA 2XRDA 5HYPA 4ZH1D 2G7IA 1QGBA 3GOVA 3K3TA 4WJG2 1E88A 3ZLEA 2XWJI 2RL0A 3F6KA 1ELVA 4IGDA 1Q3XA 3ZRZA 2Y8TA 3FGRA 2BZMA 4JHSA 4F4OC
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1FBR A;  1HFI A;  3RJ3 D;  4AYI A;  1UOT P;  4J38 B;  1GKG A;  1Z92 B;  4AYD A;  5JPM G;  2UWN A;  1OK9 A;  2W81 A;  3R62 A;  1E5G A;  3IU3 I;  1OJY A;  5HZP B;  2EHF A;  1HCC A;  1VVD A;  4PZ5 A;  5HYU B;  2B5I D;  4B2S A;  2W80 A;  2RKZ A;  1H03 P;  1E8B A;  1OJW A;  3OP8 A;  4MUC A;  1O9A A;  1H2Q P;  2JGX A;  3SW0 X;  1NWV A;  2RLQ A;  1C1Z A;  3MQL A;  1SS2 A;  3OED C;  1G4F A;  2CG6 A;  2IZ4 A;  4AYM A;  2CG7 A;  2MCY A;  3TVJ A;  2ERJ A;  3GXE A;  1U5M A;  1HFH A;  2XRB A;  3ERB A;  5FO8 C;  1OK1 A;  2YRA A;  2EC3 A;  1TPN A;  5HYT B;  3O8E B;  3INB C;  1OJV A;  1LY2 A;  3T5O A;  2O39 C;  1SRZ A;  2KMS A;  5I0Q B;  2JGW A;  3OXU D;  4CSY A;  4KKD A;  1G4G A;  3NFP I;  1TPG A;  1ZJK A;  4C16 A;  3EJH A;  2RKY A;  1OK3 A;  4K12 A;  1TPM A;  1H2P P;  2CKU A;  1GKN A;  3KZJ A;  3KXV A;  3ZD1 A;  1VVC A;  2A55 A;  4LOT A;  4LOS A;  1QUB A;  2JRA A;  2IZ3 A;  1H04 P;  1QO6 A;  1MD8 A;  1PPQ A;  3IX0 A;  3M7P A;  1GPZ A;  2YBY A;  3ZD2 A;  2WII C;  4A5W B;  1MD7 A;  4ONT D;  2LOJ A;  2QY0 A;  2RLP A;  3CAL A;  4B2R A;  4YNX A;  1OK2 A;  1CKL A;  3L89 M;  4AYE A;  4FXG G;  2XQW C;  1GHQ B;  4DJZ A;  2V8E A;  2MCZ A;  2XWB F;  2KRI A;  2XRD A;  5HYP A;  4ZH1 D;  2G7I A;  1QGB A;  3GOV A;  4WJG 2;  1E88 A;  2XWJ I;  2RL0 A;  1ELV A;  4IGD A;  1Q3X A;  3ZRZ A;  2BZM A;  4JHS A;  4F4O C; 
#chains in the Genus database with same CATH topology
 1FBR A;  1HFI A;  3RJ3 D;  4AYI A;  1UOT P;  4J38 B;  1GKG A;  1Z92 B;  4AYD A;  5JPM G;  2UWN A;  1OK9 A;  2W81 A;  3R62 A;  1E5G A;  3IU3 I;  1OJY A;  5HZP B;  2EHF A;  3ZLD A;  1HCC A;  1VVD A;  4PZ5 A;  5HYU B;  2B5I D;  4B2S A;  2W80 A;  4MSL A;  2RKZ A;  2X2Z A;  1H03 P;  1E8B A;  3NJA A;  1OJW A;  3OP8 A;  4MUC A;  1O9A A;  1H2Q P;  2JGX A;  3SW0 X;  1NWV A;  2RLQ A;  2Y8R A;  1C1Z A;  3MQL A;  1SS2 A;  3OED C;  1G4F A;  2CG6 A;  2IZ4 A;  4APL A;  4AYM A;  2CG7 A;  2MCY A;  3TVJ A;  2ERJ A;  3GXE A;  2ZYC A;  1U5M A;  1HFH A;  2XRB A;  3ERB A;  5FO8 C;  1OK1 A;  2YRA A;  2EC3 A;  1TPN A;  5HYT B;  3O8E B;  3INB C;  1OJV A;  1LY2 A;  3WSX A;  3T5O A;  2O39 C;  1SRZ A;  2KMS A;  5I0Q B;  2JGW A;  3OXU D;  4CSY A;  4KKD A;  5DN4 A;  1G4G A;  3NFP I;  4PO7 A;  1TPG A;  1ZJK A;  4C16 A;  3EJH A;  2RKY A;  1OK3 A;  4K12 A;  1TPM A;  1H2P P;  4N7E A;  2CKU A;  1GKN A;  3KZJ A;  3KXV A;  3ZD1 A;  1RLH A;  1VVC A;  2A55 A;  4LOT A;  4LOS A;  1QUB A;  3CI0 J;  2JRA A;  3VWO A;  2IZ3 A;  1H04 P;  1QO6 A;  1MD8 A;  1PPQ A;  3FGT A;  2Y8S A;  5DN5 A;  3IX0 A;  3M7P A;  1GPZ A;  2YBY A;  3ZD2 A;  2WII C;  4A5W B;  1MD7 A;  4ONT D;  2LOJ A;  2QY0 A;  2RLP A;  3CAL A;  2I2L A;  4B2R A;  4YNX A;  1OK2 A;  1CKL A;  3L89 M;  4AYE A;  4FXG G;  2XQW C;  4BWC A;  1GHQ B;  4YIZ A;  4DJZ A;  2V8E A;  2MCZ A;  2XWB F;  2KRI A;  3WSY A;  2XRD A;  5HYP A;  4ZH1 D;  2G7I A;  1QGB A;  3GOV A;  3K3T A;  4WJG 2;  1E88 A;  3ZLE A;  2XWJ I;  2RL0 A;  3F6K A;  1ELV A;  4IGD A;  1Q3X A;  3ZRZ A;  2Y8T A;  3FGR A;  2BZM A;  4JHS A;  4F4O C; 
#chains in the Genus database with same CATH homology
 1FBR A;  1HFI A;  3RJ3 D;  4AYI A;  1UOT P;  4J38 B;  1GKG A;  1Z92 B;  4AYD A;  5JPM G;  2UWN A;  1OK9 A;  2W81 A;  3R62 A;  1E5G A;  3IU3 I;  1OJY A;  5HZP B;  2EHF A;  1HCC A;  1VVD A;  4PZ5 A;  5HYU B;  2B5I D;  4B2S A;  2W80 A;  2RKZ A;  1H03 P;  1E8B A;  1OJW A;  3OP8 A;  4MUC A;  1O9A A;  1H2Q P;  2JGX A;  3SW0 X;  1NWV A;  2RLQ A;  1C1Z A;  3MQL A;  1SS2 A;  3OED C;  1G4F A;  2CG6 A;  2IZ4 A;  4AYM A;  2CG7 A;  2MCY A;  3TVJ A;  2ERJ A;  3GXE A;  1U5M A;  1HFH A;  2XRB A;  3ERB A;  5FO8 C;  1OK1 A;  2YRA A;  2EC3 A;  1TPN A;  5HYT B;  3O8E B;  3INB C;  1OJV A;  1LY2 A;  3T5O A;  2O39 C;  1SRZ A;  2KMS A;  5I0Q B;  2JGW A;  3OXU D;  4CSY A;  4KKD A;  1G4G A;  3NFP I;  1TPG A;  1ZJK A;  4C16 A;  3EJH A;  2RKY A;  1OK3 A;  4K12 A;  1TPM A;  1H2P P;  2CKU A;  1GKN A;  3KZJ A;  3KXV A;  3ZD1 A;  1VVC A;  2A55 A;  4LOT A;  4LOS A;  1QUB A;  2JRA A;  2IZ3 A;  1H04 P;  1QO6 A;  1MD8 A;  1PPQ A;  3IX0 A;  3M7P A;  1GPZ A;  2YBY A;  3ZD2 A;  2WII C;  4A5W B;  1MD7 A;  4ONT D;  2LOJ A;  2QY0 A;  2RLP A;  3CAL A;  4B2R A;  4YNX A;  1OK2 A;  1CKL A;  3L89 M;  4AYE A;  4FXG G;  2XQW C;  1GHQ B;  4DJZ A;  2V8E A;  2MCZ A;  2XWB F;  2KRI A;  2XRD A;  5HYP A;  4ZH1 D;  2G7I A;  1QGB A;  3GOV A;  4WJG 2;  1E88 A;  2XWJ I;  2RL0 A;  1ELV A;  4IGD A;  1Q3X A;  3ZRZ A;  2BZM A;  4JHS A;  4F4O C;

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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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4JHSA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations