3B9XA

Crystal structure of the e. coli pyrimidine nucleoside hydrolase yeik in complex with inosine
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
309
structure length
309
Chain Sequence
KRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYIK
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)EMPTYAH4 (127-136)AH1 (14-24)TIV1 (38-41)AH2 (43-57)S2 (29-36)3H1 (79-81)TIV2 (39-42)TI2 (83-86)S3 (63-65)TIV3 (70-73)AH5 (165-169)AH9 (210-231)3H2 (138-143)AH3 (104-114)S4 (120-123)S5 (146-150)AH10 (239-248)TI3 (160-163)TII1 (269-272)TIV5 (153-156)TI5 (267-270)TIV7 (158-161)TIV6 (157-160)AH6 (171-179)S9 (253-263)S6 (184-187)S11 (287-293)AH7 (189-193)TI4 (193-196)TIV8 (233-236)S7 (196-197)AH8 (199-208)AH11 (295-308)S10 (272-276)TI6 (276-279)TI7 (279-282)S8 (236-237)3H3 (250-252)Updating...
connected with : NaN
publication title Structural basis for substrate specificity in group I nucleoside hydrolases
pubmed doi rcsb
molecule keywords Pyrimidine-specific ribonucleoside hydrolase rihB
molecule tags Hydrolase
source organism Escherichia coli
total genus 108
structure length 309
sequence length 309
chains with identical sequence B, C, D
ec nomenclature ec 3.2.2.8: Ribosylpyrimidine nucleosidase.
pdb deposition date 2007-11-07

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 3b9xA00
3B9GA 1HOZA 4I72A 4KL0A 4I73A 3MKMA 1HP0A 4I70A 4I71A 2MASA 4KPOA 3EPWA 1R4FA 1Q8FA 1KICA 3B9XA 5TSQA 3EPXA 1EZRA 4WR2A 1KIEA 4P5FA 2C40A 4I74A 2FF1A 4KPNA 1MASA 3MKNA 2YHGA 2FF2A 3T8JA 1YOEA 3T8IA 3FZ0A 4I75A 3G5IA
chains in the Genus database with same CATH superfamily
3B9GA 1HOZA 4I72A 4KL0A 4I73A 3MKMA 1HP0A 4I70A 4I71A 2MASA 4KPOA 3EPWA 1R4FA 1Q8FA 1KICA 3B9XA 5TSQA 3EPXA 1EZRA 4WR2A 1KIEA 4P5FA 2C40A 4I74A 2FF1A 4KPNA 1MASA 3MKNA 2YHGA 2FF2A 3T8JA 1YOEA 3T8IA 3FZ0A 4I75A 3G5IA
chains in the Genus database with same CATH topology
3B9GA 1HOZA 4I72A 4KL0A 4I73A 3MKMA 1HP0A 4I70A 4I71A 2MASA 4KPOA 3EPWA 1R4FA 1Q8FA 1KICA 3B9XA 5TSQA 3EPXA 1EZRA 4WR2A 1KIEA 4P5FA 2C40A 4I74A 2FF1A 4KPNA 1MASA 3MKNA 2YHGA 2FF2A 3T8JA 1YOEA 3T8IA 3FZ0A 4I75A 3G5IA
chains in the Genus database with same CATH homology


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