5KH2 | 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	229
structure length	224
Chain Sequence	QVPAHIGIIMDGNGRWAKKRMQPRVFGHKAGMEALQTVTKAANKLGVKVITVYAFSRPDQEVKFIMNLPVEFYDNYVPELHANNVKIQMIGETDRLPKQTFEALTKAEELTKNNTGLILNFALNYGGRAEITQALKLISQDVLDAKINPGDITEELIGNYLFTQHLPKDLRDPDLIIRTSGELRLSNFLPWQGAYSELYFTDTLWPDFDEAALQEAILAYNRRH

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/5d0e39a3e830ce68657cae09/pdb.gz): 2460 ms

reading 224 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

224 atoms created

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

Time for creating model: 21 ms

Adding embedded #jmolscript: select ({0:223});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	Streptococcus pneumoniae serotype 4 (strain atcc baa-334 / tigr4)
publication title	Discovery and Characterization of a Class of Pyrazole Inhibitors of Bacterial Undecaprenyl Pyrophosphate Synthase. pubmed doi rcsb
molecule keywords	Isoprenyl transferase
total genus	84
structure length	224
sequence length	229
chains with identical sequence	B, C, D
ec nomenclature	ec 2.5.1.-:
pdb deposition date	2016-06-14

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	5kh2A00

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

#chains in the Genus database with same CATH superfamily
 4CMW A;  2VG2 A;  3WQL A;  3SGX A;  3WYI A;  1JP3 A;  5KH2 A;  5HXQ A;  5CQJ A;  4H2J A;  5HC7 A;  4H3A A;  5HXO A;  3WYJ A;  4ONC A;  4Q9M A;  3UGS A;  4H2O A;  2E9A A;  5HXP A;  1V7U A;  2E9C A;  3WQM A;  5KH4 A;  2VG1 A;  4H2M A;  1X07 A;  2VG3 A;  4H38 A;  4Q9O A;  2E98 A;  3TH8 A;  1X06 A;  2D2R A;  2E9D A;  4H8E A;  1X08 A;  3WQN A;  1X09 A;  5HXT A;  1F75 A;  3SGT A;  3SGV A;  5KH5 A;  4KT8 A;  5HC8 A;  2VG0 A;  5CQB A;  3SH0 A;  5HC6 A;  4CMV A;  4H3C A;  3QAS A;  2VFW A;  1UEH A;  2DTN A;  3WQK A;  2VG4 A;  2E99 A;  4U82 A;  4CMX A;  5HXN A; 
#chains in the Genus database with same CATH topology
 4CMW A;  2VG2 A;  3WQL A;  3SGX A;  3WYI A;  1JP3 A;  5KH2 A;  5HXQ A;  5CQJ A;  4H2J A;  5HC7 A;  4H3A A;  5HXO A;  3WYJ A;  4ONC A;  4Q9M A;  3UGS A;  4H2O A;  2E9A A;  5HXP A;  1V7U A;  2E9C A;  3WQM A;  5KH4 A;  2VG1 A;  4H2M A;  1X07 A;  2VG3 A;  4H38 A;  4Q9O A;  2E98 A;  3TH8 A;  1X06 A;  2D2R A;  2E9D A;  4H8E A;  1X08 A;  3WQN A;  1X09 A;  5HXT A;  1F75 A;  3SGT A;  3SGV A;  5KH5 A;  4KT8 A;  5HC8 A;  2VG0 A;  5CQB A;  3SH0 A;  5HC6 A;  4CMV A;  4H3C A;  3QAS A;  2VFW A;  1UEH A;  2DTN A;  3WQK A;  2VG4 A;  2E99 A;  4U82 A;  4CMX A;  5HXN A; 
#chains in the Genus database with same CATH homology
 4CMW A;  2VG2 A;  3WQL A;  3SGX A;  3WYI A;  1JP3 A;  5KH2 A;  5HXQ A;  5CQJ A;  4H2J A;  5HC7 A;  4H3A A;  5HXO A;  3WYJ A;  4ONC A;  4Q9M A;  3UGS A;  4H2O A;  2E9A A;  5HXP A;  1V7U A;  2E9C A;  3WQM A;  5KH4 A;  2VG1 A;  4H2M A;  1X07 A;  2VG3 A;  4H38 A;  4Q9O A;  2E98 A;  3TH8 A;  1X06 A;  2D2R A;  2E9D A;  4H8E A;  1X08 A;  3WQN A;  1X09 A;  5HXT A;  1F75 A;  3SGT A;  3SGV A;  5KH5 A;  4KT8 A;  5HC8 A;  2VG0 A;  5CQB A;  3SH0 A;  5HC6 A;  4CMV A;  4H3C A;  3QAS A;  2VFW A;  1UEH A;  2DTN A;  3WQK A;  2VG4 A;  2E99 A;  4U82 A;  4CMX A;  5HXN 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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5KH2A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations