3MKMA

Crystal structure of the e. coli pyrimidine nucleoside hydrolase yeik (apo-form)
Total Genus 112

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
112
sequence length
311
structure length
311
Chain Sequence
MEKRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYIK
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
EMPTYTI1 (26-29)S1 (4-10)S5 (144-150)AH5 (127-136)TI2 (83-86)AH1 (14-24)AH3 (79-82)TIV4 (85-88)AH11 (239-248)AH12 (295-309)S2 (29-36)TIV1 (38-41)TIV2 (39-42)S3 (63-65)AH4 (104-114)AH6 (165-169)TIV3 (70-73)3H1 (138-143)S6 (184-187)TIV6 (157-160)TIV7 (158-161)S10 (272-276)TI3 (160-163)AH7 (171-179)TI5 (267-270)S9 (253-263)AH8 (189-193)TI4 (193-196)S7 (196-197)S8 (236-237)AH9 (199-208)AH10 (210-231)3H2 (250-252)TI6 (276-279)TII1 (269-272)TI7 (279-282)S11 (287-293)AH2 (43-57)TIV5 (153-156)S4 (119-123)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
source organism Escherichia coli
total genus 112
structure length 311
sequence length 311
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 3mkmA00
4I75A 1R4FA 1KICA 2FF2A 1HOZA 3T8JA 4KL0A 4I74A 4I72A 4KPOA 3B9GA 3B9XA 2C40A 2FF1A 4I71A 2YHGA 3T8IA 1HP0A 1EZRA 1MASA 4I70A 1Q8FA 4KPNA 3MKMA 3EPXA 4WR2A 3MKNA 4P5FA 2MASA 5TSQA 1KIEA 3FZ0A 3G5IA 4I73A 3EPWA 1YOEA
chains in the Genus database with same CATH superfamily
4I75A 1R4FA 1KICA 2FF2A 1HOZA 3T8JA 4KL0A 4I74A 4I72A 4KPOA 3B9GA 3B9XA 2C40A 2FF1A 4I71A 2YHGA 3T8IA 1HP0A 1EZRA 1MASA 4I70A 1Q8FA 4KPNA 3MKMA 3EPXA 4WR2A 3MKNA 4P5FA 2MASA 5TSQA 1KIEA 3FZ0A 3G5IA 4I73A 3EPWA 1YOEA
chains in the Genus database with same CATH topology
4I75A 1R4FA 1KICA 2FF2A 1HOZA 3T8JA 4KL0A 4I74A 4I72A 4KPOA 3B9GA 3B9XA 2C40A 2FF1A 4I71A 2YHGA 3T8IA 1HP0A 1EZRA 1MASA 4I70A 1Q8FA 4KPNA 3MKMA 3EPXA 4WR2A 3MKNA 4P5FA 2MASA 5TSQA 1KIEA 3FZ0A 3G5IA 4I73A 3EPWA 1YOEA
chains in the Genus database with same CATH homology


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