3MKN | Genus

Total Genus 108

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	108
sequence length	310
structure length	303
Chain Sequence	KRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFEPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYIKT

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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Viewer cachePut cache://localLOAD_/file/5cff8febb8ec2d8fedb2125c/pdb.gz

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The Resolver thinks Pdb

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

Time for openFile(/file/5cff8febb8ec2d8fedb2125c/pdb.gz): 1465 ms

reading 303 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

303 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:302});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	Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures pubmed doi rcsb
molecule keywords	Putative uncharacterized protein YeiK
molecule tags	Hydrolase/hydrolase inhibitor
source organism	Escherichia coli
total genus	108
structure length	303
sequence length	310
chains with identical sequence	B, C, D
ec nomenclature	ec 3.2.2.8: Ribosylpyrimidine nucleosidase.
pdb deposition date	2010-04-15

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01156	IU_nuc_hydro	Inosine-uridine preferring nucleoside hydrolase

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase; Chain A	Ribonucleoside hydrolase-like	3mknA00

1R4FA 3G5IA 4I73A 4I71A 4KPNA 2FF2A 1HP0A 3B9XA 4I72A 3B9GA 1KICA 2FF1A 4I74A 3EPWA 4KPOA 3FZ0A 1YOEA 1EZRA 1KIEA 3MKMA 2YHGA 3EPXA 4P5FA 4I70A 3T8IA 3T8JA 1MASA 4WR2A 2C40A 2MASA 5TSQA 1HOZA 1Q8FA 4I75A 3MKNA 4KL0A
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 1R4F A;  3G5I A;  4I73 A;  4I71 A;  4KPN A;  2FF2 A;  1HP0 A;  3B9X A;  4I72 A;  3B9G A;  1KIC A;  2FF1 A;  4I74 A;  3EPW A;  4KPO A;  3FZ0 A;  1YOE A;  1EZR A;  1KIE A;  3MKM A;  2YHG A;  3EPX A;  4P5F A;  4I70 A;  3T8I A;  3T8J A;  1MAS A;  4WR2 A;  2C40 A;  2MAS A;  5TSQ A;  1HOZ A;  1Q8F A;  4I75 A;  3MKN A;  4KL0 A; 
#chains in the Genus database with same CATH topology
 1R4F A;  3G5I A;  4I73 A;  4I71 A;  4KPN A;  2FF2 A;  1HP0 A;  3B9X A;  4I72 A;  3B9G A;  1KIC A;  2FF1 A;  4I74 A;  3EPW A;  4KPO A;  3FZ0 A;  1YOE A;  1EZR A;  1KIE A;  3MKM A;  2YHG A;  3EPX A;  4P5F A;  4I70 A;  3T8I A;  3T8J A;  1MAS A;  4WR2 A;  2C40 A;  2MAS A;  5TSQ A;  1HOZ A;  1Q8F A;  4I75 A;  3MKN A;  4KL0 A; 
#chains in the Genus database with same CATH homology
 1R4F A;  3G5I A;  4I73 A;  4I71 A;  4KPN A;  2FF2 A;  1HP0 A;  3B9X A;  4I72 A;  3B9G A;  1KIC A;  2FF1 A;  4I74 A;  3EPW A;  4KPO A;  3FZ0 A;  1YOE A;  1EZR A;  1KIE A;  3MKM A;  2YHG A;  3EPX A;  4P5F A;  4I70 A;  3T8I A;  3T8J A;  1MAS A;  4WR2 A;  2C40 A;  2MAS A;  5TSQ A;  1HOZ A;  1Q8F A;  4I75 A;  3MKN A;  4KL0 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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3MKNA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations