4HGV | Genus

Total Genus 158

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	461
structure length	456
Chain Sequence	STRTETDTFGPIEVASDRYWGAQAQRSLGNFKIGWEKQPLAIVRALGIVKQAAARANMALGRLDPAIGDAIVKAAQEVIDGKLDEHFPLVVWQTGSGTQSNMNANEVVSNRAIELLGGVMGSKKPVHPNDHVNMSQSSNDTYPTAMHIACAERVIHDLLPALKHLHKALEEKVKAFDHIIKIGRTHTQDATPLTLGQEFSGYAAQVASSIKRIEMTLPGLCELAQGGTAVGTGLNAPVGFAEKVAEEIAAITGIGFTSAPNKFEALAAHDSMVFSHGAINATAAALFKIANDIRFLGSGPRSGLGELSLPENEPGSKVNPTQCEALTQVCVQVFGNHAALTFAGSQGHFELNVYNPLMAYNFLQSVQLLADAAISFTDNCVVGIEAREDNIKAALDRSLMLVTALAPKIGYDNAAKIAKTAHKNGTTLREEAVGGGYVTDEEFDAVVRPETMIGPA

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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/5d0044a8370d26bd2ca44aa1/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d0044a8370d26bd2ca44aa1/pdb.gz): 1065 ms

reading 456 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

456 atoms created

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

Time for creating model: 29 ms

Adding embedded #jmolscript: select ({0:455});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	Sinorhizobium meliloti
publication title	Crystal structure of a fumarate hydratase rcsb
molecule keywords	Fumarate hydratase class II
total genus	158
structure length	456
sequence length	461
chains with identical sequence	B, C, D
ec nomenclature	ec 4.2.1.2: Fumarate hydratase.
pdb deposition date	2012-10-08

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00206	Lyase_1	Lyase
A	PF10415	FumaraseC_C	Fumarase C C-terminus

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)	4hgvA03
1.10.275.10	Mainly Alpha	Orthogonal Bundle	Fumarase C; Chain B, domain 1	Fumarase/aspartase (N-terminal domain)	4hgvA01
1.20.200.10	Mainly Alpha	Up-down Bundle	Fumarase C; Chain A, domain 2	Fumarase/aspartase (Central domain)	4hgvA02

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

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations