3MKM | Genus

Total Genus 112

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	112
sequence length	311
structure length	311
Chain Sequence	MEKRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYIK

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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reading 311 atoms

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311 atoms created

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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
source organism	Escherichia coli
total genus	112
structure length	311
sequence length	311
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	3mkmA00

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations