1EZR | Genus

Total Genus 99

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	99
sequence length	312
structure length	312
Chain Sequence	PRKIILDCDPGIDDAVAIFLAHGNPEIELLAITTVVGNQSLEKVTQNARLVADVAGIVGVPVAAGCTKPLVRGVRNASHIHGETGMGNVSYPPEFKTKLDGRHAVQLIIDLIMSHEPKTITLVPTGGLTNIAMAVRLEPRIVDRVKEVVLMGGGYHTGNASPVAEFNVFIDPEAAHIVFNESWNVTMVGLDLTHLALATPAVQKRVREVGTKPAAFMLQILDFYTKVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELNGALTTGMTVADFRYPRPKNCRTQVAVKLDFDKFWCLVIDALERIGDP

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/5cfb180feadac7b76fe9619e/pdb.gz

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The Resolver thinks Pdb

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

Time for openFile(/file/5cfb180feadac7b76fe9619e/pdb.gz): 1370 ms

reading 312 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

312 atoms created

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

Time for creating model: 24 ms

Adding embedded #jmolscript: select ({0:311});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	Nucleoside hydrolase from Leishmania major. Cloning, expression, catalytic properties, transition state inhibitors, and the 2.5-a crystal structure. pubmed doi rcsb
molecule keywords	NUCLEOSIDE HYDROLASE
molecule tags	Hydrolase
source organism	Leishmania major
total genus	99
structure length	312
sequence length	312
chains with identical sequence	B, C, D
ec nomenclature	ec 3.2.2.2: Inosine nucleosidase.
pdb deposition date	2000-05-11

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	1ezrA00

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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1EZRA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations