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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 debug null

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AppletRegistry.checkIn(jmolApplet0__7559369275563683__)

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Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

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Jmol getValue HOVERCallback null

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Jmol getValue PICKCallback null

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Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/2xtj/A/2xtj_A.pdb.gz)

The Resolver thinks Pdb

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Time for openFile(/static/knot_data/2xtj/A/2xtj_A.pdb.gz): 288 ms

reading 242 atoms

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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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FileManager.getAtomSetCollectionFromFile(/static/knot_data/2xtj/A/2xtj_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/2xtj/A/2xtj_A.pdb.gz): 12 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

Time for creating model: 13 ms

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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

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

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

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2XTJA

Slipknot S +31

Chain Sequence

pfam database annotations

Slipknot S +3₁