5HXT | Genus

Total Genus 84

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	84
sequence length	221
structure length	221
Chain Sequence	LMPKHIALIMDGNRRWAKDKGLDVSEGYKHLFPKLKEICDISSKLGIQVITAFAFSTENWKRAKGEVDFLMQMFEELYDEFSRSGVRVSIIGCKTDLPMTLQKCIALTEETTKGNKGLHLVIALNYGGYYDILQATKSIVNKAMNGLLDVEDINKNLFDQELESKCPNPDLLIRTGGDQRVSNFLLWQLAYTEFYFTKTLFPDFGEEDLKEAIINFQQRHR

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/5d0dcdba3cf8006838bb31c0/pdb.gz): 1092 ms

reading 221 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

221 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:220});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

publication title	Crystal Structure and Potential Head-to-Middle Condensation Function of a Z,Z-Farnesyl Diphosphate Synthase doi rcsb
molecule keywords	(2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
molecule tags	Transferase
source organism	Solanum habrochaites
total genus	84
structure length	221
sequence length	221
chains with identical sequence	B
ec nomenclature	ec 2.5.1.92: (2Z,6Z)-farnesyl diphosphate synthase.
pdb deposition date	2016-01-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01255	Prenyltransf	Putative undecaprenyl diphosphate synthase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.1180.10	Alpha Beta	3-Layer(aba) Sandwich	Undecaprenyl pyrophosphate synthetase	Decaprenyl diphosphate synthase-like	5hxtA00

2E98A 3WQKA 4CMXA 5HXQA 4U82A 5CQJA 5HXNA 1F75A 5KH5A 2VG1A 4Q9MA 4CMVA 1X07A 3UGSA 3WQLA 2VG0A 3SGTA 5HXTA 2VG3A 2VFWA 3WQMA 4H2JA 4KT8A 2E9CA 5KH2A 5HC6A 2E9DA 1X09A 4ONCA 2D2RA 2E9AA 3WYJA 3SGVA 4H3AA 3TH8A 5HXPA 1X06A 5CQBA 4H2OA 5HC8A 4H38A 2E99A 4H3CA 4CMWA 1JP3A 4H2MA 3SH0A 3WQNA 1V7UA 2VG4A 1X08A 5HXOA 3WYIA 5KH4A 3QASA 1UEHA 3SGXA 2DTNA 4H8EA 5HC7A 2VG2A 4Q9OA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2E98 A;  3WQK A;  4CMX A;  5HXQ A;  4U82 A;  5CQJ A;  5HXN A;  1F75 A;  5KH5 A;  2VG1 A;  4Q9M A;  4CMV A;  1X07 A;  3UGS A;  3WQL A;  2VG0 A;  3SGT A;  5HXT A;  2VG3 A;  2VFW A;  3WQM A;  4H2J A;  4KT8 A;  2E9C A;  5KH2 A;  5HC6 A;  2E9D A;  1X09 A;  4ONC A;  2D2R A;  2E9A A;  3WYJ A;  3SGV A;  4H3A A;  3TH8 A;  5HXP A;  1X06 A;  5CQB A;  4H2O A;  5HC8 A;  4H38 A;  2E99 A;  4H3C A;  4CMW A;  1JP3 A;  4H2M A;  3SH0 A;  3WQN A;  1V7U A;  2VG4 A;  1X08 A;  5HXO A;  3WYI A;  5KH4 A;  3QAS A;  1UEH A;  3SGX A;  2DTN A;  4H8E A;  5HC7 A;  2VG2 A;  4Q9O A; 
#chains in the Genus database with same CATH topology
 2E98 A;  3WQK A;  4CMX A;  5HXQ A;  4U82 A;  5CQJ A;  5HXN A;  1F75 A;  5KH5 A;  2VG1 A;  4Q9M A;  4CMV A;  1X07 A;  3UGS A;  3WQL A;  2VG0 A;  3SGT A;  5HXT A;  2VG3 A;  2VFW A;  3WQM A;  4H2J A;  4KT8 A;  2E9C A;  5KH2 A;  5HC6 A;  2E9D A;  1X09 A;  4ONC A;  2D2R A;  2E9A A;  3WYJ A;  3SGV A;  4H3A A;  3TH8 A;  5HXP A;  1X06 A;  5CQB A;  4H2O A;  5HC8 A;  4H38 A;  2E99 A;  4H3C A;  4CMW A;  1JP3 A;  4H2M A;  3SH0 A;  3WQN A;  1V7U A;  2VG4 A;  1X08 A;  5HXO A;  3WYI A;  5KH4 A;  3QAS A;  1UEH A;  3SGX A;  2DTN A;  4H8E A;  5HC7 A;  2VG2 A;  4Q9O A; 
#chains in the Genus database with same CATH homology
 2E98 A;  3WQK A;  4CMX A;  5HXQ A;  4U82 A;  5CQJ A;  5HXN A;  1F75 A;  5KH5 A;  2VG1 A;  4Q9M A;  4CMV A;  1X07 A;  3UGS A;  3WQL A;  2VG0 A;  3SGT A;  5HXT A;  2VG3 A;  2VFW A;  3WQM A;  4H2J A;  4KT8 A;  2E9C A;  5KH2 A;  5HC6 A;  2E9D A;  1X09 A;  4ONC A;  2D2R A;  2E9A A;  3WYJ A;  3SGV A;  4H3A A;  3TH8 A;  5HXP A;  1X06 A;  5CQB A;  4H2O A;  5HC8 A;  4H38 A;  2E99 A;  4H3C A;  4CMW A;  1JP3 A;  4H2M A;  3SH0 A;  3WQN A;  1V7U A;  2VG4 A;  1X08 A;  5HXO A;  3WYI A;  5KH4 A;  3QAS A;  1UEH A;  3SGX A;  2DTN A;  4H8E A;  5HC7 A;  2VG2 A;  4Q9O 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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5HXTA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations