1YOEA

Crystal structure of a the e. coli pyrimidine nucleoside hydrolase ybek with bound ribose
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
302
Chain Sequence
GSALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIAESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA

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

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
S1 (3-9)S4 (119-123)EMPTYS2 (28-35)AH1 (13-24)AH11 (296-307)TI1 (25-28)AH2 (42-56)TIV1 (37-40)TIV2 (38-41)TI2 (58-61)TI3 (70-73)AH5 (165-169)S9 (254-259)AH3 (104-114)AH4 (127-136)TI4 (160-163)3H1 (138-143)AH6 (171-179)S5 (144-150)TIV5 (157-160)TIV8 (264-267)TIV4 (153-156)TI6 (277-280)S6 (184-187)AH7 (189-193)S7 (196-197)TIV6 (193-196)AH8 (199-208)S12 (288-294)S8 (237-238)TIV7 (234-237)AH10 (241-249)TI5 (267-270)3H2 (251-253)S10 (261-264)TIV9 (268-271)TII1 (270-273)S11 (273-276)S3 (63-65)AH9 (211-225)Updating...
connected with : NaN
publication title Crystal structure of the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose
rcsb
molecule keywords Hypothetical protein ybeK
molecule tags Hydrolase
source organism Escherichia coli
total genus 99
structure length 302
sequence length 312
ec nomenclature ec 3.2.2.8: Ribosylpyrimidine nucleosidase.
pdb deposition date 2005-01-27

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
ClassArchitectureTopologyHomologyDomain
3.90.245.10 Alpha Beta Alpha-Beta Complex Inosine-uridine Nucleoside N-ribohydrolase; Chain A Ribonucleoside hydrolase-like 1yoeA00
2FF2A 2FF1A 4I73A 3EPWA 4I71A 2YHGA 3T8JA 1Q8FA 2C40A 1R4FA 3T8IA 3FZ0A 4I74A 3MKNA 4WR2A 1KIEA 1YOEA 4I70A 2MASA 1HP0A 4KL0A 3G5IA 1HOZA 4I75A 1KICA 3EPXA 4KPNA 4KPOA 1EZRA 3B9XA 5TSQA 4P5FA 4I72A 3B9GA 1MASA 3MKMA
chains in the Genus database with same CATH superfamily
2FF2A 2FF1A 4I73A 3EPWA 4I71A 2YHGA 3T8JA 1Q8FA 2C40A 1R4FA 3T8IA 3FZ0A 4I74A 3MKNA 4WR2A 1KIEA 1YOEA 4I70A 2MASA 1HP0A 4KL0A 3G5IA 1HOZA 4I75A 1KICA 3EPXA 4KPNA 4KPOA 1EZRA 3B9XA 5TSQA 4P5FA 4I72A 3B9GA 1MASA 3MKMA
chains in the Genus database with same CATH topology
2FF2A 2FF1A 4I73A 3EPWA 4I71A 2YHGA 3T8JA 1Q8FA 2C40A 1R4FA 3T8IA 3FZ0A 4I74A 3MKNA 4WR2A 1KIEA 1YOEA 4I70A 2MASA 1HP0A 4KL0A 3G5IA 1HOZA 4I75A 1KICA 3EPXA 4KPNA 4KPOA 1EZRA 3B9XA 5TSQA 4P5FA 4I72A 3B9GA 1MASA 3MKMA
chains in the Genus database with same CATH homology


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