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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
sequence length 194
structure length 190
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
molecule tags Hydrolase
molecule keywords peptide deformylase PDF1
source organism Staphylococcus aureus
missing residues 7-10
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)
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
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; 
1LM4A 2OS0A 2OS1A 3SVJP 5JF0A 5JF6A 5JEZA 5JF3A 3SW8P 4EOXP 3STRP 5JF5A 5JF8A 1LQYA 1LM6A 2AIEP 2OKLA 2AIAA 5JF1A 1LMHA 5JEXA 5JF2A 1Q1YA 5JF7A 3U7KA 1LQWA 3U7LA 3L87A 2AI7A 3U7MA 5JF4A 3U7NA 2OS3A 2AI9A 3G6NA 5JEYA 3CMDA
similar chains in the KnotProt database (40% sequence similarity)
1LM4B 2OKLB 1LQWB 2AI9B 3G6NB 3CMDB
similar chains in the pdb database (40% sequence similarity)

 
            
               
#similar chains in the KnotProt database (40% sequence similarity)
 1LM4 A; 
               
               
#similar chains, but unknotted
 2OS0 A;  2OS1 A;  3SVJ P;  5JF0 A;  5JF6 A;  5JEZ A;  5JF3 A;  3SW8 P;  4EOX P;  3STR P;  5JF5 A;  5JF8 A;  1LQY A;  1LM6 A;  2AIE P;  2OKL A;  2AIA A;  5JF1 A;  1LMH A;  5JEX A;  5JF2 A;  1Q1Y A;  5JF7 A;  3U7K A;  1LQW A;  3U7L A;  3L87 A;  2AI7 A;  3U7M A;  5JF4 A;  3U7N A;  2OS3 A;  2AI9 A;  3G6N A;  5JEY A;  3CMD A;                               
               
           
#similar chains in the pdb database (40% sequence similarity)
 1LM4 B;  2OKL B;  1LQW B;  2AI9 B;  3G6N B;  3CMD B; 
           

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling