3SGX | Genus

Total Genus 72

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	72
sequence length	222
structure length	211
Chain Sequence	GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSELMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFAN

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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callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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Viewer cachePut cache://localLOAD_/file/5d02de9473d4fd42bc245fbb/pdb.gz

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loadScript /static/js/j2s/core/corezip.z.js

The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5d02de9473d4fd42bc245fbb/pdb.gz): 2741 ms

reading 211 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

211 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:210});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	Antibacterial drug leads targeting isoprenoid biosynthesis. pubmed doi rcsb
molecule keywords	Undecaprenyl pyrophosphate synthase
molecule tags	Transferase/transferase inhibitor
source organism	Escherichia coli
total genus	72
structure length	211
sequence length	222
chains with identical sequence	B
ec nomenclature	ec 2.5.1.31: Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-
pdb deposition date	2011-06-15

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	3sgxA00

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

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

1UEHA 1V7UA 1X06A 1X07A 2E98A 2E99A 2E9AA 2E9CA 2E9DA
similar chains in the Genus database (40% sequence similarity)

None
similar chains in the pdb database (40% sequence similarity)

#similar chains in the Genus database (40% sequence similarity)
1UEH A; 1V7U A; 1X06 A; 1X07 A; 2E98 A; 2E99 A; 2E9A A; 2E9C A; 2E9D A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)

3SGXA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations