3MKNA

Crystal structure of the e. coli pyrimidine nucleosidase yeik bound to a competitive inhibitor
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
310
structure length
303
Chain Sequence
KRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFEPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYIKT
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)TIV4 (78-81)TIV2 (39-42)TI2 (79-82)TI3 (80-83)S3 (63-65)TIV3 (70-73)AH5 (165-169)3H1 (138-143)AH3 (104-114)S5 (144-150)TI5 (160-163)TIV6 (153-156)S7 (253-263)TIV8 (158-161)TIV7 (157-160)AH6 (171-179)S6 (184-187)TI7 (276-279)TI8 (279-282)AH7 (189-193)TIV10 (226-229)AH9 (210-226)AH10 (240-248)TI6 (267-270)3H2 (250-252)TII1 (269-272)AH11 (295-308)TI4 (83-86)AH8 (199-208)TIV9 (193-196)S8 (272-276)S4 (119-123)S9 (287-293)Updating...
connected with : NaN
publication title Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures
pubmed doi rcsb
molecule keywords Putative uncharacterized protein YeiK
molecule tags Hydrolase/hydrolase inhibitor
source organism Escherichia coli
total genus 108
structure length 303
sequence length 310
chains with identical sequence B, C, D
ec nomenclature ec 3.2.2.8: Ribosylpyrimidine nucleosidase.
pdb deposition date 2010-04-15

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 3mknA00
1R4FA 3G5IA 4I73A 4I71A 4KPNA 2FF2A 1HP0A 3B9XA 4I72A 3B9GA 1KICA 2FF1A 4I74A 3EPWA 4KPOA 3FZ0A 1YOEA 1EZRA 1KIEA 3MKMA 2YHGA 3EPXA 4P5FA 4I70A 3T8IA 3T8JA 1MASA 4WR2A 2C40A 2MASA 5TSQA 1HOZA 1Q8FA 4I75A 3MKNA 4KL0A
chains in the Genus database with same CATH superfamily
1R4FA 3G5IA 4I73A 4I71A 4KPNA 2FF2A 1HP0A 3B9XA 4I72A 3B9GA 1KICA 2FF1A 4I74A 3EPWA 4KPOA 3FZ0A 1YOEA 1EZRA 1KIEA 3MKMA 2YHGA 3EPXA 4P5FA 4I70A 3T8IA 3T8JA 1MASA 4WR2A 2C40A 2MASA 5TSQA 1HOZA 1Q8FA 4I75A 3MKNA 4KL0A
chains in the Genus database with same CATH topology
1R4FA 3G5IA 4I73A 4I71A 4KPNA 2FF2A 1HP0A 3B9XA 4I72A 3B9GA 1KICA 2FF1A 4I74A 3EPWA 4KPOA 3FZ0A 1YOEA 1EZRA 1KIEA 3MKMA 2YHGA 3EPXA 4P5FA 4I70A 3T8IA 3T8JA 1MASA 4WR2A 2C40A 2MASA 5TSQA 1HOZA 1Q8FA 4I75A 3MKNA 4KL0A
chains in the Genus database with same CATH homology


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