3NDAA

Crystal structure of serpin from tick ixodes ricinus
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Slipknot S -31
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
-31 235-344 110 345-377 1-221 222-234 221 32 slipknot
Chain Sequence
MQEEAKLTKANNRFGLRLLRALPSGPEKNVFFSPYSVSTAMGMAFAGARGQTQQELSQGLGFSDVDLTDAGVLDAYTHHTERLKSTPSNSTLDVANAAAIQRTLALLNSYESALQSSFGAELHKVDFAGEPQAAVDFVNNWVKRKTHDKIEKLFNEPLDPDTLLVLLNAIYFKGEWNTAFVKEHTEKRQFFNGGVTPVEVDTMRLEARIKYRFFDDLQVEVVELPYRGLDYTMAILLPKENTGVEGLKQNLTIDRFQNYLSDLRERKITVLLPKFKLETKYSLKAPLQSLGIKQIFESGADLSGINDGSLRVSAVEHKAVVEVNEEGTVAAATTGVVIVPY---PEPVVFRVDHPFLFFIRNTRTDDIFFVGQVNKL
sequence length 377
structure length 374
publication title A tick salivary protein targets cathepsin G and chymase and inhibits host inflammation and platelet aggregation.
pubmed doi rcsb
molecule tags Hydrolase inhibitor
molecule keywords Serpin-2
source organism Ixodes ricinus
missing residues 342-344
ec nomenclature
pdb deposition date 2010-06-07
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00079 Serpin Serpin (serine protease inhibitor)
Image from the rcsb pdb (www.rcsb.org)
Whole chain analysis
Subchain analysis 

Knotoid cutoff: 0.5



Knotoid matrix content: 1

Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
2.1m 226-341 116 1-220, 347-374 221-225, 342-346 220 28 slipknot
view details
3.1m 232-343 112 1-224, 354-374 225-231, 344-353 224 21 slipknot
view details
3.1m 233-371 139 372-374 1-226 227-232 226 2 slipknot
view details
2.1m 236-341 106 1-229, 347-374 230-235, 342-346 229 28 slipknot
view details
2.1m 237-342 106 1-235, 347-374 236-236, 343-346 235 28 slipknot
view details
3.1m 235-347 113 1-231, 353-374 232-234, 348-352 231 22 slipknot
cath code
ClassArchitectureTopologyHomologyDomain
2.30.39.10 Mainly Beta Roll Alpha-1-antitrypsin; domain 1 Alpha-1-antitrypsin, domain 1 3ndaA02
3.30.497.10 Alpha Beta 2-Layer Sandwich Antithrombin; Chain I, domain 2 Antithrombin, subunit I, domain 2 3ndaA01
2WXZC 1BY7A 3NDAA
chains in the KnotProt database with same CATH superfamily
2WXZC 1BY7A 3NDAA
chains in the KnotProt database with same CATH topology
2WXZC 1BY7A 3NDAA
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 2WXZ C;  1BY7 A;  3NDA A; 
#chains in the KnotProt database with same CATH topology
 2WXZ C;  1BY7 A;  3NDA A; 
#chains in the KnotProt database with same CATH homology
 2WXZ C;  1BY7 A;  3NDA A; 
3NDAA 1BY7A 2XN6A 5CDZA 5OM2A 3NDDA 2XN7A 2RIVA 4X30A 2ARRA 5OM5A 3DY0A 4YIAA 1JRRA 4KDSA 4P0FA 5NBUA 3B9FI 2H4PA 5OM7A 2XN5A 3NE4A 3F02A 5NBVA 1LJ5A 2ARQA 5OM6A 1OVAA 1OVAB 1OVAC 1HLEA 3LW2A 4DTEA 1A7CA 4PYWA 1UHGA 5OM3A 4ZK3A 2V95A 3FGQA 2RIWA 4ZK0A 2H4QA 4IF8A 2QUGA 1YXAA 4G8RA 1AS4A 1SEKA 1K9OI 2OL2A 4Y40A 1QLPA 1WZ9A 4AFXA 4Y3KA 5OM8A 3CVMA 2XN3A 4AQHA 1HP7A 1OPHA 1QMNA 4DY0A 1OC0A 1DVNA 3Q02A 1JTIA 1IZ2A 5CE0A 3DRMA 3CAAA 4IC0A 2VDYA 4BB2A 5CDXA 3PB1I 3UT3A 3F1SA 2HI9A 3Q03A 1DVMA 1LQ8A 3CWLA 9PAIA 2ACHA 1OO8A 2ZV6A 1EZXA 3EOXA 3CWMA 1ATUA 1QMBA 4AJTA 2H4RA 4AJUA 4GA7A 3R4LA 3NDFA 4CAAA 3DLWA 7APIA 1XU8A 4DY7C 1XQGA 4G8OA 1PSIA 1D5SA 9APIA 1XQJA 2CEOA 1DB2A 5BRRI 8APIA 1KCTA 3H5CA 1B3KA 5IO1A 3F5NA 3DRUA 2DUTA 2D26A 3T1PA 1C5GA
similar chains in the KnotProt database (40% sequence similarity)
4P0OA 3NDAB 4C41A 3F02B 6FTPA 2VDXA 2VDXB 5OM6C 1OVAD 4DTEB 1UHGB 1UHGC 1UHGD 3FGQB 4IF8B 1YXAB 4G8RB 2OL2B 4Y40B 1WZ9B 4Y3KB 3CVMB 4AQHB 4AQHC 5HGCA 4DY0B 3Q02B 1JTIB 5CE0B 4IC0B 4IC0C 4IC0D 2VDYB 3UT3B 3UT3C 3UT3D 2HI9B 2HI9C 3Q03B 1DVMB 1DVMC 1DVMD 1LQ8C 1LQ8E 1LQ8G 2ZV6B 2ZV6C 5EI0A 5EI0E 4GA7B 4C49A 4C49B 4C49C 4C49D 1XU8B 4DY7F 1XQGB 4G8OB 4G8OC 4G8OD 3VVJA 3VVJB 3VVJC 2CEOB 1DB2B 1B3KB 1B3KC 1B3KD 5IO1B 3F5NB 3F5NC 3F5ND 3F5NE 3DRUB 3DRUC 2DUTB 2DUTC 2DUTD
similar chains in the pdb database (40% sequence similarity)

 
            
               
#similar chains in the KnotProt database (40% sequence similarity)
 3NDA A;  1BY7 A; 
               
               
#similar chains, but unknotted
 2XN6 A;  5CDZ A;  5OM2 A;  3NDD A;  2XN7 A;  2RIV A;  4X30 A;  2ARR A;  5OM5 A;  3DY0 A;  4YIA A;  1JRR A;  4KDS A;  4P0F A;  5NBU A;  3B9F I;  2H4P A;  5OM7 A;  2XN5 A;  3NE4 A;  3F02 A;  5NBV A;  1LJ5 A;  2ARQ A;  5OM6 A;  1OVA A;  1OVA B;  1OVA C;  1HLE A;  3LW2 A;  4DTE A;  1A7C A;  4PYW A;  1UHG A;  5OM3 A;  4ZK3 A;  2V95 A;  3FGQ A;  2RIW A;  4ZK0 A;  2H4Q A;  4IF8 A;  2QUG A;  1YXA A;  4G8R A;  1AS4 A;  1SEK A;  1K9O I;  2OL2 A;  4Y40 A;  1QLP A;  1WZ9 A;  4AFX A;  4Y3K A;  5OM8 A;  3CVM A;  2XN3 A;  4AQH A;  1HP7 A;  1OPH A;  1QMN A;  4DY0 A;  1OC0 A;  1DVN A;  3Q02 A;  1JTI A;  1IZ2 A;  5CE0 A;  3DRM A;  3CAA A;  4IC0 A;  2VDY A;  4BB2 A;  5CDX A;  3PB1 I;  3UT3 A;  3F1S A;  2HI9 A;  3Q03 A;  1DVM A;  1LQ8 A;  3CWL A;  9PAI A;  2ACH A;  1OO8 A;  2ZV6 A;  1EZX A;  3EOX A;  3CWM A;  1ATU A;  1QMB A;  4AJT A;  2H4R A;  4AJU A;  4GA7 A;  3R4L A;  3NDF A;  4CAA A;  3DLW A;  7API A;  1XU8 A;  4DY7 C;  1XQG A;  4G8O A;  1PSI A;  1D5S A;  9API A;  1XQJ A;  2CEO A;  1DB2 A;  5BRR I;  8API A;  1KCT A;  3H5C A;  1B3K A;  5IO1 A;  3F5N A;  3DRU A;  2DUT A;  2D26 A;  3T1P A;  1C5G A;                               
               
           
#similar chains in the pdb database (40% sequence similarity)
 4P0O A;  3NDA B;  4C41 A;  3F02 B;  6FTP A;  2VDX A;  2VDX B;  5OM6 C;  1OVA D;  4DTE B;  1UHG B;  1UHG C;  1UHG D;  3FGQ B;  4IF8 B;  1YXA B;  4G8R B;  2OL2 B;  4Y40 B;  1WZ9 B;  4Y3K B;  3CVM B;  4AQH B;  4AQH C;  5HGC A;  4DY0 B;  3Q02 B;  1JTI B;  5CE0 B;  4IC0 B;  4IC0 C;  4IC0 D;  2VDY B;  3UT3 B;  3UT3 C;  3UT3 D;  2HI9 B;  2HI9 C;  3Q03 B;  1DVM B;  1DVM C;  1DVM D;  1LQ8 C;  1LQ8 E;  1LQ8 G;  2ZV6 B;  2ZV6 C;  5EI0 A;  5EI0 E;  4GA7 B;  4C49 A;  4C49 B;  4C49 C;  4C49 D;  1XU8 B;  4DY7 F;  1XQG B;  4G8O B;  4G8O C;  4G8O D;  3VVJ A;  3VVJ B;  3VVJ C;  2CEO B;  1DB2 B;  1B3K B;  1B3K C;  1B3K D;  5IO1 B;  3F5N B;  3F5N C;  3F5N D;  3F5N E;  3DRU B;  3DRU C;  2DUT B;  2DUT C;  2DUT D; 
           

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