4DZ4A

X-ray crystal structure of a hypothetical agmatinase from burkholderia thailandensis
Warning
  • Chain breaks within knot 31 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Slipknot S +31
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
+31 30-167 138 1-27, 279-316 28-29, 168-278 27 38 slipknot
Chain Sequence
TLYGDGAIRRPSVYGSSIENTYAGVLSFMRRNYTRDLDGVDVVVSGVPLDLATTFRSGARLGPSAVRAASVQLAELNPYPWGFDPFDDLAVIDYGDCWFDAHHPLSIKPAIVEHARTILQSDARMLTLGGDHYITYPLLIAHAQKYGKPLSLIHFDAHCDTWAD---DSLNHGTMFYKAVKDGLIDPKASVQVGIRTWNDDYLGINVLDAAWVHEHGARATLERIESIVGGRPAYLTFDIDCLDPAFAPGTGTPVAGGLSSAQALAIVRGLGGVNLIGADVVEVAPAYDQSEITAIAAAHVACDLLCLWRQRKAGA
Whole chain analysis
Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1

Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
2.1 32-237 206 1-25, 253-313 26-31, 238-252 25 61 slipknot
view details
2.1 32-97 66 1-26, 124-313 27-31, 98-123 26 190 slipknot
view details
2.1 32-159 128 1-26, 181-313 27-31, 160-180 26 133 slipknot
sequence length 316
structure length 313
publication title Combining functional and structural genomics to sample the essential Burkholderia structome.
pubmed doi rcsb
molecule tags Hydrolase
molecule keywords Agmatinase
source organism Burkholderia thailandensis
missing residues 165-167
total genus Genus: 119
ec nomenclature ec 3.5.3.11: Agmatinase.
pdb deposition date 2012-02-29
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00491 Arginase Arginase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.800.10 Alpha Beta 3-Layer(aba) Sandwich Arginase; Chain A Arginase; Chain A 4dz4A00
4DZ4A 1GQ6A 1WOHA 1WOIA 1WOGA 1GQ7A
chains in the KnotProt database with same CATH superfamily
4DZ4A 1GQ6A 1WOHA 1WOIA 1WOGA 1GQ7A
chains in the KnotProt database with same CATH topology
4DZ4A 1GQ6A 1WOHA 1WOIA 1WOGA 1GQ7A
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 4DZ4 A;  1GQ6 A;  1WOH A;  1WOI A;  1WOG A;  1GQ7 A; 
#chains in the KnotProt database with same CATH topology
 4DZ4 A;  1GQ6 A;  1WOH A;  1WOI A;  1WOG A;  1GQ7 A; 
#chains in the KnotProt database with same CATH homology
 4DZ4 A;  1GQ6 A;  1WOH A;  1WOI A;  1WOG A;  1GQ7 A; 
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the KnotProt database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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