1Q8FA

Crystal structure of the e.coli pyrimidine nucleoside hydrolase yeik
Total Genus 108

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
108
sequence length
308
structure length
308
Chain Sequence
KRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYI
5010015020025030030025020015010050
020406080100Genus Matrix

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 (4-10)TI1 (26-29)EMPTYAH5 (127-136)AH1 (14-24)TIV1 (38-41)AH2 (43-57)S2 (29-36)TIV2 (39-42)AH3 (79-82)TI2 (83-86)S3 (63-65)TIV3 (70-73)AH6 (165-169)AH10 (210-231)3H1 (138-143)AH4 (104-114)S4 (119-123)AH11 (239-248)S5 (144-150)TI3 (160-163)TII1 (269-272)TIV5 (153-156)TI5 (267-270)TIV7 (158-161)TIV6 (157-160)AH7 (171-179)S9 (253-263)S6 (184-187)S11 (287-293)AH8 (189-193)TI4 (193-196)TIV8 (233-236)S7 (196-197)AH9 (199-208)AH12 (295-308)S10 (272-276)TI6 (276-279)TI7 (279-282)S8 (236-237)3H2 (250-252)Updating...
connected with : NaN
publication title Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy.
pubmed doi rcsb
molecule keywords Pyrimidine nucleoside hydrolase
molecule tags Hydrolase
source organism Escherichia coli
total genus 108
structure length 308
sequence length 308
chains with identical sequence B, C, D
ec nomenclature ec 3.2.2.8: Ribosylpyrimidine nucleosidase.
pdb deposition date 2003-08-21

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 1q8fA00
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
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 topology
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 homology


 
#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)

 
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#similar chains, but unknotted
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