3G5I | Genus

Total Genus 100

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	100
sequence length	310
structure length	305
Chain Sequence	ALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA

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/5cfef275906694d364cc7a67/pdb.gz

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The Resolver thinks Pdb

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

Time for openFile(/file/5cfef275906694d364cc7a67/pdb.gz): 1199 ms

reading 305 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

305 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:304});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	Crystal structure of the RihA nucleoside hydrolase bound to a competitive inhibitor rcsb
molecule keywords	Pyrimidine-specific ribonucleoside hydrolase rihA
molecule tags	Hydrolase
source organism	Escherichia coli
total genus	100
structure length	305
sequence length	310
chains with identical sequence	B, C, D
ec nomenclature	ec 3.2.2.8: Ribosylpyrimidine nucleosidase.
pdb deposition date	2009-02-05

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	3g5iA00

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

#chains in the Genus database with same CATH superfamily
 3EPX A;  1EZR A;  1YOE A;  4I70 A;  3MKN A;  2MAS A;  2FF1 A;  3T8J A;  2FF2 A;  1Q8F A;  1KIC A;  4KPN A;  3B9X A;  1MAS A;  4I75 A;  4I72 A;  5TSQ A;  1HP0 A;  4WR2 A;  4I73 A;  4P5F A;  4KPO A;  4I71 A;  2YHG A;  3B9G A;  4I74 A;  1HOZ A;  3MKM A;  1KIE A;  3T8I A;  2C40 A;  3G5I A;  3EPW A;  3FZ0 A;  4KL0 A;  1R4F A; 
#chains in the Genus database with same CATH topology
 3EPX A;  1EZR A;  1YOE A;  4I70 A;  3MKN A;  2MAS A;  2FF1 A;  3T8J A;  2FF2 A;  1Q8F A;  1KIC A;  4KPN A;  3B9X A;  1MAS A;  4I75 A;  4I72 A;  5TSQ A;  1HP0 A;  4WR2 A;  4I73 A;  4P5F A;  4KPO A;  4I71 A;  2YHG A;  3B9G A;  4I74 A;  1HOZ A;  3MKM A;  1KIE A;  3T8I A;  2C40 A;  3G5I A;  3EPW A;  3FZ0 A;  4KL0 A;  1R4F A; 
#chains in the Genus database with same CATH homology
 3EPX A;  1EZR A;  1YOE A;  4I70 A;  3MKN A;  2MAS A;  2FF1 A;  3T8J A;  2FF2 A;  1Q8F A;  1KIC A;  4KPN A;  3B9X A;  1MAS A;  4I75 A;  4I72 A;  5TSQ A;  1HP0 A;  4WR2 A;  4I73 A;  4P5F A;  4KPO A;  4I71 A;  2YHG A;  3B9G A;  4I74 A;  1HOZ A;  3MKM A;  1KIE A;  3T8I A;  2C40 A;  3G5I A;  3EPW A;  3FZ0 A;  4KL0 A;  1R4F 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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3G5IA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations