2XTJ | KnotProt

2XTJA

The crystal structure of pcsk9 in complex with 1d05 fab

Image from the <span class='capital'>rcsb pdb</span> (www.rcsb.org)

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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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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Help Knotting data interpretation Full screen

					Knot core range	Knot core length	Knot tails range	Slipknot tails range	Slipknot loops range	N-end length	C-end length	Type
view details				+3₁	29-99	71	1-28	102-268	100-101	28	167	slipknot

Chain Sequence

PWN--------------------SLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDQASKCDSHGTHLAGVVSGRD------AGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLILFSAKD

Whole chain analysis

Help Knotoid data interpretation Full screen

Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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Jmol getValue APPLETREADYCallback Jmol._readyCallback

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callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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The Resolver thinks Pdb

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reading 242 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

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242 atoms created

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The Resolver thinks Pdb

Time for openFile(/static/knot_data/2xtj/A/2xtj_A.pdb.gz): 9 ms

reading 242 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

242 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

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Help Knotoid subchains data interpretation Full screen

					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	Class	Architecture	Topology	Homology	Domain
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

1OF1A 1E2KA 4IVQA 1E2MA 3M5DA 1P6XA 3L06A 1R4MB 1KI2A 3L04A 1YVEI 1F48A 1E2LA 3L02A 3FR7A 2KI5A 3FSGA 1KI7A 1KI4A 1R4NB 1KI3A 3F0TA 1GKUB 4JBXA 4IVRA 1P72A 3KZMA 1E2JA 1VTKA 1E2NA 3KZNA 1YH1A 3FR8A 2FG6C 1KI8A 3RDPA 1P73A 1II9A 1E2HA 3M4NA 1DBIA 1E2IA 1P75A 2G7MC 3KZKA 3VTKA 1JS1X 3KZCA 3L05A 2VTKA 2XTJA 1QHIA 4JBYA 1QMGA 3KZOA 3M5CA 1OSNA 3M4JA 1E2PA 4IVPA 1KI6B 1KI6A 1P7CA 1LNSA 1YRLA 1KIMA
chains in the KnotProt database with same CATH topology

3M5DA 3L06A 3L04A 3L02A 3FSGA 1GKUB 3KZMA 3KZNA 1YH1A 2FG6C 1DBIA 3KZKA 2G7MC 1JS1X 3KZCA 3L05A 2XTJA 3KZOA 3M5CA 3M4JA 1LNSA 3M4NA
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
 1OF1 A;  1E2K A;  4IVQ A;  1E2M A;  3M5D A;  1P6X A;  3L06 A;  1R4M B;  1KI2 A;  3L04 A;  1YVE I;  1F48 A;  1E2L A;  3L02 A;  3FR7 A;  2KI5 A;  3FSG A;  1KI7 A;  1KI4 A;  1R4N B;  1KI3 A;  3F0T A;  1GKU B;  4JBX A;  4IVR A;  1P72 A;  3KZM A;  1E2J A;  1VTK A;  1E2N A;  3KZN A;  1YH1 A;  3FR8 A;  2FG6 C;  1KI8 A;  3RDP A;  1P73 A;  1II9 A;  1E2H A;  3M4N A;  1DBI A;  1E2I A;  1P75 A;  2G7M C;  3KZK A;  3VTK A;  1JS1 X;  3KZC A;  3L05 A;  2VTK A;  2XTJ A;  1QHI A;  4JBY A;  1QMG A;  3KZO A;  3M5C A;  1OSN A;  3M4J A;  1E2P A;  4IVP A;  1KI6 B;  1KI6 A;  1P7C A;  1LNS A;  1YRL A;  1KIM A; 
#chains in the KnotProt database with same CATH homology
 3M5D A;  3L06 A;  3L04 A;  3L02 A;  3FSG A;  1GKU B;  3KZM A;  3KZN A;  1YH1 A;  2FG6 C;  1DBI A;  3KZK A;  2G7M C;  1JS1 X;  3KZC A;  3L05 A;  2XTJ A;  3KZO A;  3M5C A;  3M4J A;  1LNS A;  3M4N A;

None 2W2MA 2W2NA 2W2OA 2W2PA 2W2QA 4NMXB 6XIBB 6XICB 6XIDB
similar chains in the KnotProt database (40% sequence similarity)

None
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)

#similar chains, but unknotted
6XID B; 
#similar chains in the pdb database (40% sequence similarity)

How to cite

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling

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2XTJA

Slipknot S +31

Chain Sequence

pfam database annotations

Slipknot S +3₁