2XTJA

The crystal structure of pcsk9 in complex with 1d05 fab
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 29-99 71 1-28 102-268 100-101 28 167 slipknot
Chain Sequence
PWN--------------------SLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDQASKCDSHGTHLAGVVSGRD------AGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLILFSAKD
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 10-69 60 1-9 78-242 70-77 9 165 slipknot
view details
1.1 15-70 56 1-9, 78-242 10-14, 71-77 9 165 slipknot
sequence length 268
structure length 242
publication title A Pcsk9-Binding Antibody that Structurally Mimics the Egf(A) Domain of Ldl-Receptor Reduces Ldl Cholesterol in Vivo.
pubmed doi rcsb
molecule tags Hydrolase/antibody
molecule keywords PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
source organism Homo sapiens
missing residues 4-23, 59-64
total genus Genus: 83
ec nomenclature ec 3.4.21.-:
pdb deposition date 2010-10-10
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00082 Peptidase_S8 Subtilase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.50.200 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Rossmann fold 2xtjA00
2XTJA 1DBIA
chains in the KnotProt database with same CATH superfamily
3VTKA 4IVPA 3FR8A 1JS1X 1DBIA 1YH1A 2XTJA 3L06A 3M4NA 1GKUB 4IVRA 1KI8A 3KZCA 1QMGA 3M5DA 1E2IA 3L02A 1E2JA 2G7MC 1KI7A 4JBYA 3RDPA 1P72A 1LNSA 3KZNA 3KZMA 3L04A 1F48A 1P75A 1QHIA 1E2NA 1KI2A 2KI5A 3FSGA 1KIMA 1KI6B 1YRLA 1P6XA 1P73A 3KZKA 3L05A 1YVEI 1P7CA 1VTKA 3M4JA 1E2KA 4IVQA 2FG6C 1E2HA 3F0TA 1KI4A 1E2PA 1R4MB 1KI6A 3M5CA 1OF1A 1II9A 3KZOA 1R4NB 1E2LA 1KI3A 1OSNA 2VTKA 3FR7A 4JBXA 1E2MA
chains in the KnotProt database with same CATH topology
1JS1X 1YH1A 2XTJA 3L06A 3M4NA 1GKUB 3KZCA 3M5DA 3L02A 2G7MC 3KZMA 1LNSA 3KZNA 3L04A 3FSGA 3L05A 3KZKA 3M4JA 2FG6C 3M5CA 3KZOA 1DBIA
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 2XTJ A;  1DBI A; 
#chains in the KnotProt database with same CATH topology
 3VTK A;  4IVP A;  3FR8 A;  1JS1 X;  1DBI A;  1YH1 A;  2XTJ A;  3L06 A;  3M4N A;  1GKU B;  4IVR A;  1KI8 A;  3KZC A;  1QMG A;  3M5D A;  1E2I A;  3L02 A;  1E2J A;  2G7M C;  1KI7 A;  4JBY A;  3RDP A;  1P72 A;  1LNS A;  3KZN A;  3KZM A;  3L04 A;  1F48 A;  1P75 A;  1QHI A;  1E2N A;  1KI2 A;  2KI5 A;  3FSG A;  1KIM A;  1KI6 B;  1YRL A;  1P6X A;  1P73 A;  3KZK A;  3L05 A;  1YVE I;  1P7C A;  1VTK A;  3M4J A;  1E2K A;  4IVQ A;  2FG6 C;  1E2H A;  3F0T A;  1KI4 A;  1E2P A;  1R4M B;  1KI6 A;  3M5C A;  1OF1 A;  1II9 A;  3KZO A;  1R4N B;  1E2L A;  1KI3 A;  1OSN A;  2VTK A;  3FR7 A;  4JBX A;  1E2M A; 
#chains in the KnotProt database with same CATH homology
 1JS1 X;  1YH1 A;  2XTJ A;  3L06 A;  3M4N A;  1GKU B;  3KZC A;  3M5D A;  3L02 A;  2G7M C;  3KZM A;  1LNS A;  3KZN A;  3L04 A;  3FSG A;  3L05 A;  3KZK A;  3M4J A;  2FG6 C;  3M5C A;  3KZO A;  1DBI 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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