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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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