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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 83
Slipknot S +31

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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 29-99 71 1-28 102-268 100-101 28 167 slipknot
Chain Sequence
PWN--------------------SLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDQASKCDSHGTHLAGVVSGRD------AGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLILFSAKD
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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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
1F48A 4IVPA 3L02A 1VTKA 3KZNA 1YH1A 1KI8A 2KI5A 1E2NA 2VTKA 1QHIA 2XTJA 3M5CA 3RDPA 1YVEI 1E2JA 1II9A 1E2PA 3FSGA 3M4NA 1E2HA 1KI7A 1OF1A 1E2KA 4JBXA 3M5DA 1OSNA 3F0TA 1KI4A 4JBYA 1E2LA 1P75A 1P7CA 1GKUB 3KZMA 1KI6A 3L04A 3VTKA 1R4MB 4IVQA 3FR7A 1JS1X 1E2IA 3L05A 3M4JA 1DBIA 1KI6B 3KZCA 3KZKA 1P6XA 1E2MA 1LNSA 1P73A 1YRLA 2FG6C 1P72A 4IVRA 1R4NB 1KI2A 1KIMA 3KZOA 3L06A 1QMGA 3FR8A 2G7MC 1KI3A
chains in the KnotProt database with same CATH topology
3L02A 3KZNA 1YH1A 3M5CA 2XTJA 3FSGA 3M4NA 3M5DA 3KZMA 3L04A 1JS1X 3M4JA 3L05A 1DBIA 3KZCA 3KZKA 1LNSA 2FG6C 3L06A 3KZOA 2G7MC 1GKUB
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
 1F48 A;  4IVP A;  3L02 A;  1VTK A;  3KZN A;  1YH1 A;  1KI8 A;  2KI5 A;  1E2N A;  2VTK A;  1QHI A;  2XTJ A;  3M5C A;  3RDP A;  1YVE I;  1E2J A;  1II9 A;  1E2P A;  3FSG A;  3M4N A;  1E2H A;  1KI7 A;  1OF1 A;  1E2K A;  4JBX A;  3M5D A;  1OSN A;  3F0T A;  1KI4 A;  4JBY A;  1E2L A;  1P75 A;  1P7C A;  1GKU B;  3KZM A;  1KI6 A;  3L04 A;  3VTK A;  1R4M B;  4IVQ A;  3FR7 A;  1JS1 X;  1E2I A;  3L05 A;  3M4J A;  1DBI A;  1KI6 B;  3KZC A;  3KZK A;  1P6X A;  1E2M A;  1LNS A;  1P73 A;  1YRL A;  2FG6 C;  1P72 A;  4IVR A;  1R4N B;  1KI2 A;  1KIM A;  3KZO A;  3L06 A;  1QMG A;  3FR8 A;  2G7M C;  1KI3 A; 
#chains in the KnotProt database with same CATH homology
 3L02 A;  3KZN A;  1YH1 A;  3M5C A;  2XTJ A;  3FSG A;  3M4N A;  3M5D A;  3KZM A;  3L04 A;  1JS1 X;  3M4J A;  3L05 A;  1DBI A;  3KZC A;  3KZK A;  1LNS A;  2FG6 C;  3L06 A;  3KZO A;  2G7M C;  1GKU B;
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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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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling