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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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