2DYUA

Helicobacter pylori formamidase amif contains a fine-tuned cysteine-glutamate-lysine catalytic triad
Total Genus 102
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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
102
sequence length
322
structure length
322
Chain Sequence
GFLVAAIQFPVPIVNSRKDIDHNIESIIRTLHATKAGYPGVELIIFPEYSTQGLNTAKWLSEEFLLDVPGKETELYAKACKEAKVYGVFSIMERNPDSNKNPYNTAIIIDPQGEIILKYRKLFPWNPIEPWYPGDLGMPVCEGPGGSKLAVCICHDGMIPELAREAAYKGCNVYIRISGYSTQVNDQWILTNRSNAWHNLMYTVSVNLAGYDNVFYYFGEGQICNFDGTTLVQGHRNPWEIVTGEIYPKMADNARLSWGLENNIYNLGHRGYVAKPGGEHDAGLTYIKDLAAGKYKLPWEDHMKIKDGSIYGYPTTGGRFGK
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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
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molecule tags Hydrolase
molecule keywords Formamidase
publication title Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad
pubmed doi rcsb
source organism Helicobacter pylori
total genus 102
structure length 322
sequence length 322
chains with identical sequence B
ec nomenclature ec 3.5.1.49: Formamidase.
pdb deposition date 2006-09-18

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00795 CN_hydrolase Carbon-nitrogen hydrolase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.60.110.10 Alpha Beta 4-Layer Sandwich Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase Carbon-nitrogen hydrolase 2dyuA01
3KI8A 3SDBA 3SYTA 3SZGA 4F4HA 5JQNA 2W1VA 2E2LA 3DLAA 4CYFA 2E2KA 4KZFA 4IZTA 2GGLA 2GGKA 3KLCA 5H8IA 4GYNA 4HG5A 5H8KA 1UF7A 1UF5A 5H8JA 3WUYA 4CYGA 4IZVA 1FO6A 1F89A 3IW3A 2VHIA 1EMSA 4GYLA 4HG3A 3N05A 5H8LA 3IVZA 2UXYA 1J31A 4HGDA 2PLQA 2DYUA 1UF4A 2E11A 4IZSA 2DYVA 1UF8A 3P8KA 1ERZA 2VHHA 4H5UA 4LF0A 3SEQA 3HKXA 3SEZA 3ILVA 4IZUA 4CYYA 4IZWA 5KHAA
chains in the Genus database with same CATH superfamily
3KI8A 3SDBA 3SYTA 3SZGA 4F4HA 5JQNA 2W1VA 2E2LA 3DLAA 4CYFA 2E2KA 4KZFA 4IZTA 2GGLA 2GGKA 3KLCA 5H8IA 4GYNA 4HG5A 5H8KA 1UF7A 1UF5A 5H8JA 3WUYA 4CYGA 4IZVA 1FO6A 1F89A 3IW3A 2VHIA 1EMSA 4GYLA 4HG3A 3N05A 5H8LA 3IVZA 2UXYA 1J31A 4HGDA 2PLQA 2DYUA 1UF4A 2E11A 4IZSA 2DYVA 1UF8A 3P8KA 1ERZA 2VHHA 4H5UA 4LF0A 3SEQA 3HKXA 3SEZA 3ILVA 4IZUA 4CYYA 4IZWA 5KHAA
chains in the Genus database with same CATH topology
3KI8A 3SDBA 3SYTA 3SZGA 4F4HA 5JQNA 2W1VA 2E2LA 3DLAA 4CYFA 2E2KA 4KZFA 4IZTA 2GGLA 2GGKA 3KLCA 5H8IA 4GYNA 4HG5A 5H8KA 1UF7A 1UF5A 5H8JA 3WUYA 4CYGA 4IZVA 1FO6A 1F89A 3IW3A 2VHIA 1EMSA 4GYLA 4HG3A 3N05A 5H8LA 3IVZA 2UXYA 1J31A 4HGDA 2PLQA 2DYUA 1UF4A 2E11A 4IZSA 2DYVA 1UF8A 3P8KA 1ERZA 2VHHA 4H5UA 4LF0A 3SEQA 3HKXA 3SEZA 3ILVA 4IZUA 4CYYA 4IZWA 5KHAA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3KI8 A;  3SDB A;  3SYT A;  3SZG A;  4F4H A;  5JQN A;  2W1V A;  2E2L A;  3DLA A;  4CYF A;  2E2K A;  4KZF A;  4IZT A;  2GGL A;  2GGK A;  3KLC A;  5H8I A;  4GYN A;  4HG5 A;  5H8K A;  1UF7 A;  1UF5 A;  5H8J A;  3WUY A;  4CYG A;  4IZV A;  1FO6 A;  1F89 A;  3IW3 A;  2VHI A;  1EMS A;  4GYL A;  4HG3 A;  3N05 A;  5H8L A;  3IVZ A;  2UXY A;  1J31 A;  4HGD A;  2PLQ A;  2DYU A;  1UF4 A;  2E11 A;  4IZS A;  2DYV A;  1UF8 A;  3P8K A;  1ERZ A;  2VHH A;  4H5U A;  4LF0 A;  3SEQ A;  3HKX A;  3SEZ A;  3ILV A;  4IZU A;  4CYY A;  4IZW A;  5KHA A; 
#chains in the Genus database with same CATH topology
 3KI8 A;  3SDB A;  3SYT A;  3SZG A;  4F4H A;  5JQN A;  2W1V A;  2E2L A;  3DLA A;  4CYF A;  2E2K A;  4KZF A;  4IZT A;  2GGL A;  2GGK A;  3KLC A;  5H8I A;  4GYN A;  4HG5 A;  5H8K A;  1UF7 A;  1UF5 A;  5H8J A;  3WUY A;  4CYG A;  4IZV A;  1FO6 A;  1F89 A;  3IW3 A;  2VHI A;  1EMS A;  4GYL A;  4HG3 A;  3N05 A;  5H8L A;  3IVZ A;  2UXY A;  1J31 A;  4HGD A;  2PLQ A;  2DYU A;  1UF4 A;  2E11 A;  4IZS A;  2DYV A;  1UF8 A;  3P8K A;  1ERZ A;  2VHH A;  4H5U A;  4LF0 A;  3SEQ A;  3HKX A;  3SEZ A;  3ILV A;  4IZU A;  4CYY A;  4IZW A;  5KHA A; 
#chains in the Genus database with same CATH homology
 3KI8 A;  3SDB A;  3SYT A;  3SZG A;  4F4H A;  5JQN A;  2W1V A;  2E2L A;  3DLA A;  4CYF A;  2E2K A;  4KZF A;  4IZT A;  2GGL A;  2GGK A;  3KLC A;  5H8I A;  4GYN A;  4HG5 A;  5H8K A;  1UF7 A;  1UF5 A;  5H8J A;  3WUY A;  4CYG A;  4IZV A;  1FO6 A;  1F89 A;  3IW3 A;  2VHI A;  1EMS A;  4GYL A;  4HG3 A;  3N05 A;  5H8L A;  3IVZ A;  2UXY A;  1J31 A;  4HGD A;  2PLQ A;  2DYU A;  1UF4 A;  2E11 A;  4IZS A;  2DYV A;  1UF8 A;  3P8K A;  1ERZ A;  2VHH A;  4H5U A;  4LF0 A;  3SEQ A;  3HKX A;  3SEZ A;  3ILV A;  4IZU A;  4CYY A;  4IZW A;  5KHA 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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