4WR2 | Genus

Total Genus 89

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	89
sequence length	318
structure length	308
Chain Sequence	KAIRPLASATPIILDCDPGHDDAISLILALSSERLNPLAVTTSAGNQTPDKTLNNALRILTLLNRADMPVAGGAVKPLARELIIAGPKLPDPSFDPLTQNAIELMAEKVRQSAVPVTLVPSGPLTNIALFIANYPELHSKVERIVLMGGAAGVGNWTPAAEFNIFVDPEAADMVFKSGIPITMCGLDVTHEAQIMDEDIERIRAIPNPVAQCVAELLDFFMIYHRDPKWGFTGAPLHDPCTIAWLLKPELFTAQECWVGVETKGEYTQGMTVVDRYQLTGKTANATVLFDLDRQGFVDLIVDCLSAYN

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/5d00c0f5127ba3e1f221c442/pdb.gz): 1055 ms

reading 308 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

308 atoms created

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

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:307});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 a putative pyrimidine-specific ribonucleoside hydrolase (RihA) Protein from Shewanella loihica PV-4 (SHEW_0697, Target PSI-029635) with divalent cation and PEG 400 bound at the active site rcsb
molecule keywords	Pyrimidine-specific ribonucleoside hydrolase RihA
molecule tags	Hydrolase
source organism	Shewanella loihica
total genus	89
structure length	308
sequence length	318
ec nomenclature	ec 3.2.-.-:
pdb deposition date	2014-10-22

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	4wr2A00

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

#chains in the Genus database with same CATH superfamily
 3EPX A;  4P5F A;  1HOZ A;  3FZ0 A;  2FF2 A;  2MAS A;  4I70 A;  3EPW A;  3MKN A;  2C40 A;  1YOE A;  4I72 A;  1MAS A;  4KL0 A;  4I71 A;  3B9X A;  1KIE A;  4I73 A;  1Q8F A;  3MKM A;  1HP0 A;  3T8I A;  4KPO A;  4WR2 A;  3G5I A;  5TSQ A;  4I74 A;  4KPN A;  1EZR A;  4I75 A;  1KIC A;  2FF1 A;  2YHG A;  1R4F A;  3B9G A;  3T8J A; 
#chains in the Genus database with same CATH topology
 3EPX A;  4P5F A;  1HOZ A;  3FZ0 A;  2FF2 A;  2MAS A;  4I70 A;  3EPW A;  3MKN A;  2C40 A;  1YOE A;  4I72 A;  1MAS A;  4KL0 A;  4I71 A;  3B9X A;  1KIE A;  4I73 A;  1Q8F A;  3MKM A;  1HP0 A;  3T8I A;  4KPO A;  4WR2 A;  3G5I A;  5TSQ A;  4I74 A;  4KPN A;  1EZR A;  4I75 A;  1KIC A;  2FF1 A;  2YHG A;  1R4F A;  3B9G A;  3T8J A; 
#chains in the Genus database with same CATH homology
 3EPX A;  4P5F A;  1HOZ A;  3FZ0 A;  2FF2 A;  2MAS A;  4I70 A;  3EPW A;  3MKN A;  2C40 A;  1YOE A;  4I72 A;  1MAS A;  4KL0 A;  4I71 A;  3B9X A;  1KIE A;  4I73 A;  1Q8F A;  3MKM A;  1HP0 A;  3T8I A;  4KPO A;  4WR2 A;  3G5I A;  5TSQ A;  4I74 A;  4KPN A;  1EZR A;  4I75 A;  1KIC A;  2FF1 A;  2YHG A;  1R4F A;  3B9G A;  3T8J 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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4WR2A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations