5KH5 | Genus

Total Genus 82

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	82
sequence length	232
structure length	230
Chain Sequence	TQVPAHIGIIMDGNGRWAKKRMQPRVFGHKAGMEALQTVTKAANKLGVKVITVYAFSTENRPDQEVKFIMNLPVEFYDNYVPELHANNVKIQMIGETDRLPKQTFEALTKAEELTKNNTGLILNFALNYGGRAEITQALKLISQDVLDAKINPGDITEELIGNYLFTQHLPKDLRDPDLIIRTSGELRLSNFLPWQGAYSELYFTDTLWPDFDEAALQEAILAYNRRHRR

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/5d0e389ae830ce68657cadcb/pdb.gz): 2466 ms

reading 230 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

230 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:229});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/transferase inhibitor
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	82
structure length	230
sequence length	232
chains with identical sequence	B
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	5kh5A00

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

#chains in the Genus database with same CATH superfamily
 5HC8 A;  5HC7 A;  5CQJ A;  5HXT A;  5HC6 A;  3WQM A;  4Q9O A;  4KT8 A;  3SGX A;  2VG4 A;  2D2R A;  4H2O A;  4H3A A;  4ONC A;  4H38 A;  1UEH A;  1X08 A;  2VFW A;  2VG2 A;  3WYI A;  3WQK A;  5KH2 A;  2VG1 A;  4H2J A;  2VG3 A;  2E99 A;  4U82 A;  5HXQ A;  4H3C A;  5KH4 A;  3WQN A;  2VG0 A;  2E9D A;  3WQL A;  1X09 A;  3QAS A;  2E9A A;  4H2M A;  2E9C A;  1X07 A;  2E98 A;  5HXN A;  1V7U A;  5CQB A;  3SH0 A;  3WYJ A;  1F75 A;  3TH8 A;  4H8E A;  1X06 A;  4Q9M A;  4CMV A;  1JP3 A;  3SGT A;  3SGV A;  4CMW A;  5HXO A;  3UGS A;  4CMX A;  5KH5 A;  2DTN A;  5HXP A; 
#chains in the Genus database with same CATH topology
 5HC8 A;  5HC7 A;  5CQJ A;  5HXT A;  5HC6 A;  3WQM A;  4Q9O A;  4KT8 A;  3SGX A;  2VG4 A;  2D2R A;  4H2O A;  4H3A A;  4ONC A;  4H38 A;  1UEH A;  1X08 A;  2VFW A;  2VG2 A;  3WYI A;  3WQK A;  5KH2 A;  2VG1 A;  4H2J A;  2VG3 A;  2E99 A;  4U82 A;  5HXQ A;  4H3C A;  5KH4 A;  3WQN A;  2VG0 A;  2E9D A;  3WQL A;  1X09 A;  3QAS A;  2E9A A;  4H2M A;  2E9C A;  1X07 A;  2E98 A;  5HXN A;  1V7U A;  5CQB A;  3SH0 A;  3WYJ A;  1F75 A;  3TH8 A;  4H8E A;  1X06 A;  4Q9M A;  4CMV A;  1JP3 A;  3SGT A;  3SGV A;  4CMW A;  5HXO A;  3UGS A;  4CMX A;  5KH5 A;  2DTN A;  5HXP A; 
#chains in the Genus database with same CATH homology
 5HC8 A;  5HC7 A;  5CQJ A;  5HXT A;  5HC6 A;  3WQM A;  4Q9O A;  4KT8 A;  3SGX A;  2VG4 A;  2D2R A;  4H2O A;  4H3A A;  4ONC A;  4H38 A;  1UEH A;  1X08 A;  2VFW A;  2VG2 A;  3WYI A;  3WQK A;  5KH2 A;  2VG1 A;  4H2J A;  2VG3 A;  2E99 A;  4U82 A;  5HXQ A;  4H3C A;  5KH4 A;  3WQN A;  2VG0 A;  2E9D A;  3WQL A;  1X09 A;  3QAS A;  2E9A A;  4H2M A;  2E9C A;  1X07 A;  2E98 A;  5HXN A;  1V7U A;  5CQB A;  3SH0 A;  3WYJ A;  1F75 A;  3TH8 A;  4H8E A;  1X06 A;  4Q9M A;  4CMV A;  1JP3 A;  3SGT A;  3SGV A;  4CMW A;  5HXO A;  3UGS A;  4CMX A;  5KH5 A;  2DTN A;  5HXP 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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5KH5A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations