1LM4A

Structure of peptide deformylase from staphylococcus aureus at 1.45 a
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 7-76 70 1-6 82-194 77-81 6 113 slipknot
Chain Sequence
GSDKIH----HMLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV
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
2.1m 7-69 63 1-6 79-190 70-78 6 112 slipknot
missing residues 7-10
publication title Structure analysis of peptide deformylases from streptococcus pneumoniae,staphylococcus aureus, thermotoga maritima, and pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase
pubmed doi rcsb
structure length 190
molecule tags Hydrolase
source organism Staphylococcus aureus
sequence length 194
molecule keywords peptide deformylase PDF1
ec nomenclature ec 3.5.1.88: Peptide deformylase.
pdb deposition date 2002-04-30
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01327 Pep_deformylase Polypeptide deformylase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.45.10 Alpha Beta Alpha-Beta Complex Peptide Deformylase Peptide Deformylase 1lm4A00
1LM4A
chains in the KnotProt database with same CATH superfamily
1LM4A
chains in the KnotProt database with same CATH topology
1LM4A
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 1LM4 A; 
#chains in the KnotProt database with same CATH topology
 1LM4 A; 
#chains in the KnotProt database with same CATH homology
 1LM4 A; 
...loading similar chains, please wait...
similar chains in the KnotProt database (?% sequence similarity)
...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

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

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling