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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
4IVRA 1OF1A 3KZNA 1QMGA 1YH1A 1KI7A 3KZOA 2FG7C 3FR7A 2KI5A 2FG7X 3KZMA 1YRLA 1E2KA 1E2LA 3F0TA 3M5DA 4JBYA 4IVQA 1E2MA 1KIMA 1KI6B 1II9A 1VTKA 1GKUB 1P72A 3M4NA 4JBXA 1R4NB 1KI3A 3M5CA 1JS1X 1P7CA 3L02A 1KI8A 1LNSA 3L05A 1E2JA 1E2NA 1KI6A 3M4JA 1OSNA 1R4MB 2XTJA 3L04A 1KI4A 1QHIA 1P6XA 1P73A 3FSGA 2VTKA 1KI2A 3KZCA 1E2HA 4IVPA 1YVEI 1E2IA 3VTKA 3FR8A 2G7MC 2FG6C 1DBIA 1E2PA 1P75A 1F48A 3L06A 3KZKA 3RDPA
chains in the KnotProt database with same CATH topology
3KZNA 1YH1A 3KZOA 2FG7C 2FG7X 3KZMA 3M5DA 1GKUB 3M4NA 3M5CA 1JS1X 3L02A 3L05A 1LNSA 3M4JA 2XTJA 3L04A 3FSGA 3KZCA 2G7MC 2FG6C 1DBIA 3L06A 3KZKA
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
 4IVR A;  1OF1 A;  3KZN A;  1QMG A;  1YH1 A;  1KI7 A;  3KZO A;  2FG7 C;  3FR7 A;  2KI5 A;  2FG7 X;  3KZM A;  1YRL A;  1E2K A;  1E2L A;  3F0T A;  3M5D A;  4JBY A;  4IVQ A;  1E2M A;  1KIM A;  1KI6 B;  1II9 A;  1VTK A;  1GKU B;  1P72 A;  3M4N A;  4JBX A;  1R4N B;  1KI3 A;  3M5C A;  1JS1 X;  1P7C A;  3L02 A;  1KI8 A;  1LNS A;  3L05 A;  1E2J A;  1E2N A;  1KI6 A;  3M4J A;  1OSN A;  1R4M B;  2XTJ A;  3L04 A;  1KI4 A;  1QHI A;  1P6X A;  1P73 A;  3FSG A;  2VTK A;  1KI2 A;  3KZC A;  1E2H A;  4IVP A;  1YVE I;  1E2I A;  3VTK A;  3FR8 A;  2G7M C;  2FG6 C;  1DBI A;  1E2P A;  1P75 A;  1F48 A;  3L06 A;  3KZK A;  3RDP A; 
#chains in the KnotProt database with same CATH homology
 3KZN A;  1YH1 A;  3KZO A;  2FG7 C;  2FG7 X;  3KZM A;  3M5D A;  1GKU B;  3M4N A;  3M5C A;  1JS1 X;  3L02 A;  3L05 A;  1LNS A;  3M4J A;  2XTJ A;  3L04 A;  3FSG A;  3KZC A;  2G7M C;  2FG6 C;  1DBI A;  3L06 A;  3KZK 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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