5HW2 | Genus

Total Genus 147

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	147
sequence length	438
structure length	419
Chain Sequence	MIKRYDVAEISKIWADENKYAKMLEVELAILEALEDRMVPKGTAAEIRARAQIRPERVDEIEKVTKHDIIAFCTSIAEQFTAETGKFFHFGVTSSDIIDSALSLQIRDSMSYVIKDLEALCDSLLTKAEETKEIITMGRSHGMFAEPMSFGQKFLGAYVEFKRRLKDLKDFQKDGLTVQFSGAVGNYCILTTEDEKKAADILGLPVEEVSTQVIPRDRIAKLISIHGLIASAIERLAVEIRHLHRSDVFEVYEGFKKNPISTENLTGMARMLRSHVSIALENCVLWHERDISHSSAERFYLPDNFGIMVYALRRMKNTIDNLVVQRDIIEDRVRSTSAYLSSFYLHFLVANTPFMREDCYKIVQQVESFSKKLQKVMHDEHNIILDIPEMDFEGIKKTYLKEIDHVFDRSVKARGENLY

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/5d0dccca3cf8006838bb31a6/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d0dccca3cf8006838bb31a6/pdb.gz): 1895 ms

reading 419 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

419 atoms created

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

Time for creating model: 28 ms

Adding embedded #jmolscript: select ({0:418});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	Lyase
source organism	Francisella tularensis subsp. tularensis (strain schu s4 / schu 4)
publication title	Crystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with fumaric acid rcsb
molecule keywords	Adenylosuccinate lyase
total genus	147
structure length	419
sequence length	438
chains with identical sequence	B, C, D
ec nomenclature	ec 4.3.2.2: Adenylosuccinate lyase.
pdb deposition date	2016-01-28

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00206	Lyase_1	Lyase

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.40.30	Mainly Alpha	Orthogonal Bundle	Ribonucleotide Reductase Protein R1; domain 1	Fumarase/aspartase (C-terminal domain)	5hw2A03
1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C; Chain B, domain 1	Fumarase/aspartase (N-terminal domain)	5hw2A01
1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C; Chain A, domain 2	Fumarase/aspartase (Central domain)	5hw2A02

1JSWA 2YIIA 1J3UA 5EYTA 1U16A 1Q5NA 3R6VA 2O7FA 3TV2A 1VDKA 2NYFA 5HW2A 4HGVA 1FUOA 3BHGA 1K7WA 3KDZA 3RRPA 3OCFA 4NSLA 1YFEA 1GK2A 1TJ7A 1RE5A 3UNVA 4FFXA 2QGAB 3OCEA 5D6BA 1FUPA 2FUSA 2O7DA 2J91A 3E04A 2X75A 4C5RA 2PFMA 2O78A 3NO9A 4EEIA 2RJSA 1TJVA 2E9FA 1B8FA 3C8TA 4FLCA 1YISA 1HY1A 4ADLA 2RJRA 1HY0A 1GK3A 2QVEA 1YFMA 2PTRA 1Y2MA 3GTDA 5F91A 1AUWA 4ADMA 1FURA 4BABA 3KDYA 2HVGA 5F92A 4EFCA 2O7EA 1W27A 3R6YA 1C3UA 3R6QA 4BAAA 1GKJA 4CQ5A 1C3CA 2O7BA 1K62A 1XWOA 4C5UA 4V2QA 4APBA 2PTSA 2O6YA 4APAA 3NZ4A 3RD8A 1U15A 4C5SA 1KQ7A 2NYNA 3GZHA 1I0AA 5EYVA 4MX2A 1T6JA 1DOFA 1T6PA 1GKMA 1DCNA 3CZOA 1TJWA 1FUQA 1EB4A 2PTQA 2OHYA 4C6GA 1TJUA 2VD6A 4NLEA 4V2RA 3QBPA
chains in the Genus database with same CATH superfamily

1JSWA 2JAUA 2YIIA 1J3UA 2YV5A 5EYTA 1U16A 1Z4IA 1Q5NA 3R6VA 2O7FA 3F4SA 4WNLA 3TV2A 2D28C 5M0JA 1VDKA 2NYFA 5HW2A 4HGVA 1Z4JA 2FENA 1FUOA 3BHGA 1K7WA 3KDZA 3RRPA 2RCNA 3OCFA 4NSLA 1Z4LA 4L6CA 2I7DA 1YFEA 1GK2A 1TJ7A 1RE5A 1XMCA 3UNVA 1XMDA 1Z4QA 4FFXA 3CRW1 1XL8A 5M0IA 1Z4MA 2QGAB 3OCEA 5D6BA 4IQJM 1FUPA 2FUSA 2O7DA 4MWOA 2J91A 1U0LA 3E04A 2X75A 4C5RA 2FELA 4MUMA 2JARA 2PFMA 2O78A 3NO9A 4EEIA 2RJSA 3U13A 3BWVA 3F4TA 1TJVA 2E9FA 3F4RA 3C8TA 1B8FA 4FLCA 1T9HA 4YIHA 1Q92A 1HY1A 1YISA 4ADLA 2RJRA 4L57A 1HY0A 1GK3A 2VL7A 2QVEA 1YFMA 2PTRA 4E88A 3GTDA 1Y2MA 5F91A 1AUWA 4ADMA 1FURA 4BABA 3KDYA 1Z4PX 2HVGA 5F92A 4EFCA 2O7EA 1W27A 3R6YA 1C3UA 3R6QA 4BAAA 2JAWA 1GKJA 4CQ5A 1C3CA 2O7BA 1K62A 1XWOA 4C5UA 4V2QA 4APBA 2PTSA 3CI0K 4APAA 2O6YA 2D27A 4NFLA 1XL7A 3NZ4A 3RD8A 1Q91A 1U15A 4C5SA 5H8WA 1KQ7A 1MH9A 3U19A 2VSFA 2NYNA 3GZHA 1I0AA 5EYVA 3CRVA 4YIKA 4MX2A 1T6JA 1DOFA 1T6PA 1GKMA 1DCNA 3CZOA 1TJWA 2JAOA 1FUQA 1EB4A 2PTQA 2OHYA 4C6GA 4A15A 1TJUA 1Z4KA 4L6AA 1XLYA 2VD6A 4NLEA 4V2RA 1IW7D 3QBPA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1JSW A;  2YII A;  1J3U A;  5EYT A;  1U16 A;  1Q5N A;  3R6V A;  2O7F A;  3TV2 A;  1VDK A;  2NYF A;  5HW2 A;  4HGV A;  1FUO A;  3BHG A;  1K7W A;  3KDZ A;  3RRP A;  3OCF A;  4NSL A;  1YFE A;  1GK2 A;  1TJ7 A;  1RE5 A;  3UNV A;  4FFX A;  2QGA B;  3OCE A;  5D6B A;  1FUP A;  2FUS A;  2O7D A;  2J91 A;  3E04 A;  2X75 A;  4C5R A;  2PFM A;  2O78 A;  3NO9 A;  4EEI A;  2RJS A;  1TJV A;  2E9F A;  1B8F A;  3C8T A;  4FLC A;  1YIS A;  1HY1 A;  4ADL A;  2RJR A;  1HY0 A;  1GK3 A;  2QVE A;  1YFM A;  2PTR A;  1Y2M A;  3GTD A;  5F91 A;  1AUW A;  4ADM A;  1FUR A;  4BAB A;  3KDY A;  2HVG A;  5F92 A;  4EFC A;  2O7E A;  1W27 A;  3R6Y A;  1C3U A;  3R6Q A;  4BAA A;  1GKJ A;  4CQ5 A;  1C3C A;  2O7B A;  1K62 A;  1XWO A;  4C5U A;  4V2Q A;  4APB A;  2PTS A;  2O6Y A;  4APA A;  3NZ4 A;  3RD8 A;  1U15 A;  4C5S A;  1KQ7 A;  2NYN A;  3GZH A;  1I0A A;  5EYV A;  4MX2 A;  1T6J A;  1DOF A;  1T6P A;  1GKM A;  1DCN A;  3CZO A;  1TJW A;  1FUQ A;  1EB4 A;  2PTQ A;  2OHY A;  4C6G A;  1TJU A;  2VD6 A;  4NLE A;  4V2R A;  3QBP A; 
#chains in the Genus database with same CATH topology
 1JSW A;  2JAU A;  2YII A;  1J3U A;  2YV5 A;  5EYT A;  1U16 A;  1Z4I A;  1Q5N A;  3R6V A;  2O7F A;  3F4S A;  4WNL A;  3TV2 A;  2D28 C;  5M0J A;  1VDK A;  2NYF A;  5HW2 A;  4HGV A;  1Z4J A;  2FEN A;  1FUO A;  3BHG A;  1K7W A;  3KDZ A;  3RRP A;  2RCN A;  3OCF A;  4NSL A;  1Z4L A;  4L6C A;  2I7D A;  1YFE A;  1GK2 A;  1TJ7 A;  1RE5 A;  1XMC A;  3UNV A;  1XMD A;  1Z4Q A;  4FFX A;  3CRW 1;  1XL8 A;  5M0I A;  1Z4M A;  2QGA B;  3OCE A;  5D6B A;  4IQJ M;  1FUP A;  2FUS A;  2O7D A;  4MWO A;  2J91 A;  1U0L A;  3E04 A;  2X75 A;  4C5R A;  2FEL A;  4MUM A;  2JAR A;  2PFM A;  2O78 A;  3NO9 A;  4EEI A;  2RJS A;  3U13 A;  3BWV A;  3F4T A;  1TJV A;  2E9F A;  3F4R A;  3C8T A;  1B8F A;  4FLC A;  1T9H A;  4YIH A;  1Q92 A;  1HY1 A;  1YIS A;  4ADL A;  2RJR A;  4L57 A;  1HY0 A;  1GK3 A;  2VL7 A;  2QVE A;  1YFM A;  2PTR A;  4E88 A;  3GTD A;  1Y2M A;  5F91 A;  1AUW A;  4ADM A;  1FUR A;  4BAB A;  3KDY A;  1Z4P X;  2HVG A;  5F92 A;  4EFC A;  2O7E A;  1W27 A;  3R6Y A;  1C3U A;  3R6Q A;  4BAA A;  2JAW A;  1GKJ A;  4CQ5 A;  1C3C A;  2O7B A;  1K62 A;  1XWO A;  4C5U A;  4V2Q A;  4APB A;  2PTS A;  3CI0 K;  4APA A;  2O6Y A;  2D27 A;  4NFL A;  1XL7 A;  3NZ4 A;  3RD8 A;  1Q91 A;  1U15 A;  4C5S A;  5H8W A;  1KQ7 A;  1MH9 A;  3U19 A;  2VSF A;  2NYN A;  3GZH A;  1I0A A;  5EYV A;  3CRV A;  4YIK A;  4MX2 A;  1T6J A;  1DOF A;  1T6P A;  1GKM A;  1DCN A;  3CZO A;  1TJW A;  2JAO A;  1FUQ A;  1EB4 A;  2PTQ A;  2OHY A;  4C6G A;  4A15 A;  1TJU A;  1Z4K A;  4L6A A;  1XLY A;  2VD6 A;  4NLE A;  4V2R A;  1IW7 D;  3QBP A; 
#chains in the Genus database with same CATH homology
 1JSW A;  2YII A;  1J3U A;  5EYT A;  1U16 A;  1Q5N A;  3R6V A;  2O7F A;  3TV2 A;  1VDK A;  2NYF A;  5HW2 A;  4HGV A;  1FUO A;  3BHG A;  1K7W A;  3KDZ A;  3RRP A;  3OCF A;  4NSL A;  1YFE A;  1GK2 A;  1TJ7 A;  1RE5 A;  3UNV A;  4FFX A;  2QGA B;  3OCE A;  5D6B A;  1FUP A;  2FUS A;  2O7D A;  2J91 A;  3E04 A;  2X75 A;  4C5R A;  2PFM A;  2O78 A;  3NO9 A;  4EEI A;  2RJS A;  1TJV A;  2E9F A;  1B8F A;  3C8T A;  4FLC A;  1YIS A;  1HY1 A;  4ADL A;  2RJR A;  1HY0 A;  1GK3 A;  2QVE A;  1YFM A;  2PTR A;  1Y2M A;  3GTD A;  5F91 A;  1AUW A;  4ADM A;  1FUR A;  4BAB A;  3KDY A;  2HVG A;  5F92 A;  4EFC A;  2O7E A;  1W27 A;  3R6Y A;  1C3U A;  3R6Q A;  4BAA A;  1GKJ A;  4CQ5 A;  1C3C A;  2O7B A;  1K62 A;  1XWO A;  4C5U A;  4V2Q A;  4APB A;  2PTS A;  2O6Y A;  4APA A;  3NZ4 A;  3RD8 A;  1U15 A;  4C5S A;  1KQ7 A;  2NYN A;  3GZH A;  1I0A A;  5EYV A;  4MX2 A;  1T6J A;  1DOF A;  1T6P A;  1GKM A;  1DCN A;  3CZO A;  1TJW A;  1FUQ A;  1EB4 A;  2PTQ A;  2OHY A;  4C6G A;  1TJU A;  2VD6 A;  4NLE A;  4V2R A;  3QBP 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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5HW2A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations