1X09 | Genus

Total Genus 87

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	87
sequence length	231
structure length	231
Chain Sequence	LSEKLPAHGCRHVAIIMAGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANR

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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reading 231 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

231 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:230});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	Transferase
source organism	Escherichia coli
publication title	Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis. pubmed doi rcsb
molecule keywords	Undecaprenyl pyrophosphate synthetase
total genus	87
structure length	231
sequence length	231
ec nomenclature	ec 2.5.1.31: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-
pdb deposition date	2005-03-15

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	1x09A00

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

#chains in the Genus database with same CATH superfamily
 2VG0 A;  1UEH A;  5HC6 A;  4H2J A;  1F75 A;  5KH2 A;  5KH4 A;  5CQB A;  2E99 A;  1X06 A;  2VFW A;  3WQK A;  2E9A A;  3SGX A;  5CQJ A;  4U82 A;  5HXQ A;  4CMV A;  1V7U A;  3UGS A;  4CMX A;  5HXT A;  5HXN A;  3WQM A;  3WQL A;  2VG3 A;  3WYJ A;  4H3C A;  4H38 A;  5HC8 A;  3WYI A;  1X08 A;  4KT8 A;  2D2R A;  4Q9M A;  2E9D A;  3SGT A;  4H2M A;  3TH8 A;  5HXO A;  1X07 A;  2VG1 A;  5HXP A;  3WQN A;  4CMW A;  1X09 A;  2E9C A;  2VG4 A;  4ONC A;  5KH5 A;  4H3A A;  4H8E A;  4H2O A;  3SGV A;  2E98 A;  3QAS A;  5HC7 A;  1JP3 A;  3SH0 A;  4Q9O A;  2DTN A;  2VG2 A; 
#chains in the Genus database with same CATH topology
 2VG0 A;  1UEH A;  5HC6 A;  4H2J A;  1F75 A;  5KH2 A;  5KH4 A;  5CQB A;  2E99 A;  1X06 A;  2VFW A;  3WQK A;  2E9A A;  3SGX A;  5CQJ A;  4U82 A;  5HXQ A;  4CMV A;  1V7U A;  3UGS A;  4CMX A;  5HXT A;  5HXN A;  3WQM A;  3WQL A;  2VG3 A;  3WYJ A;  4H3C A;  4H38 A;  5HC8 A;  3WYI A;  1X08 A;  4KT8 A;  2D2R A;  4Q9M A;  2E9D A;  3SGT A;  4H2M A;  3TH8 A;  5HXO A;  1X07 A;  2VG1 A;  5HXP A;  3WQN A;  4CMW A;  1X09 A;  2E9C A;  2VG4 A;  4ONC A;  5KH5 A;  4H3A A;  4H8E A;  4H2O A;  3SGV A;  2E98 A;  3QAS A;  5HC7 A;  1JP3 A;  3SH0 A;  4Q9O A;  2DTN A;  2VG2 A; 
#chains in the Genus database with same CATH homology
 2VG0 A;  1UEH A;  5HC6 A;  4H2J A;  1F75 A;  5KH2 A;  5KH4 A;  5CQB A;  2E99 A;  1X06 A;  2VFW A;  3WQK A;  2E9A A;  3SGX A;  5CQJ A;  4U82 A;  5HXQ A;  4CMV A;  1V7U A;  3UGS A;  4CMX A;  5HXT A;  5HXN A;  3WQM A;  3WQL A;  2VG3 A;  3WYJ A;  4H3C A;  4H38 A;  5HC8 A;  3WYI A;  1X08 A;  4KT8 A;  2D2R A;  4Q9M A;  2E9D A;  3SGT A;  4H2M A;  3TH8 A;  5HXO A;  1X07 A;  2VG1 A;  5HXP A;  3WQN A;  4CMW A;  1X09 A;  2E9C A;  2VG4 A;  4ONC A;  5KH5 A;  4H3A A;  4H8E A;  4H2O A;  3SGV A;  2E98 A;  3QAS A;  5HC7 A;  1JP3 A;  3SH0 A;  4Q9O A;  2DTN A;  2VG2 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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1X09A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations