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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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