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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
1DBIA 2XTJA
chains in the KnotProt database with same CATH superfamily
3RDPA 3L04A 1E2HA 1VTKA 1YRLA 3L02A 3M5CA 1KI8A 2XTJA 1E2JA 2G7MC 1P7CA 1KIMA 1YVEI 3F0TA 1E2PA 1KI6A 4IVRA 1KI3A 1P72A 3KZNA 3M5DA 1E2NA 1P73A 1R4MB 1JS1X 3FR7A 3KZMA 1E2IA 1GKUB 3KZOA 4JBXA 1KI6B 1E2LA 1E2MA 1KI7A 2VTKA 1P75A 3L06A 2KI5A 1YH1A 3FR8A 3M4NA 4JBYA 4IVQA 1E2KA 1OF1A 3M4JA 1II9A 1KI4A 1KI2A 1P6XA 1R4NB 1QMGA 4IVPA 3L05A 1QHIA 2FG6C 3KZCA 3KZKA 1OSNA 1DBIA 1LNSA 3FSGA 3VTKA 1F48A
chains in the KnotProt database with same CATH topology
3L04A 3M5CA 3L02A 2XTJA 2G7MC 3FSGA 3KZNA 3M5DA 1JS1X 3KZMA 1GKUB 3KZOA 3L06A 1YH1A 3M4NA 3M4JA 3L05A 2FG6C 3KZKA 1DBIA 1LNSA 3KZCA
chains in the KnotProt database with same CATH homology

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