5CQJ | Genus

Total Genus 80

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	80
sequence length	228
structure length	212
Chain Sequence	LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE

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/5d00dbf582694ae9a44e0db6/pdb.gz): 1270 ms

reading 212 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

212 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:211});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	Antagonism screen for inhibitors of bacterial cell wall biogenesis uncovers an inhibitor of undecaprenyl diphosphate synthase. pubmed doi rcsb
molecule keywords	Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-f
molecule tags	Transferase/transferase inhibitor
source organism	Escherichia coli (strain k12)
total genus	80
structure length	212
sequence length	228
chains with identical sequence	B
ec nomenclature	ec 2.5.1.31: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-
pdb deposition date	2015-07-21

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	5cqjA00

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations