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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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