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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VPS10P DOMAIN OF HUMAN SORTILIN/NTS3 IN COMPLEX WITH TRIAZOLONE 1
 
Authors :  J. L. Andersen, D. Strandbygaard, S. Thirup
Date :  23 Dec 16  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Receptor, Vsp10P, Sortilin, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Andersen, S. Lindberg, M. Langgard, P. J. Maltas, L. C. B. Rnn, C. Bundgaard, D. Strandbygaard, S. Thirup, S. P. Watson
The Identification Of Novel Acid Isostere Based Inhibitors Of The Vps10P Family Sorting Receptor Sortilin.
Bioorg. Med. Chem. Lett. V. 27 2629 2017
PubMed-ID: 28462834  |  Reference-DOI: 10.1016/J.BMCL.2017.02.028

(-) Compounds

Molecule 1 - SORTILIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: SORT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 100 KDA NT RECEPTOR,GLYCOPROTEIN 95,GP95,NEUROTENSIN RECEPTOR 3,NTR3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PGE1Ligand/IonTRIETHYLENE GLYCOL
3Q9Z1Ligand/Ion3-(3-METHYLBUTYL)-4~{H}-1,2,3-TRIAZOL-5-ONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:272 , SER A:283 , ARG A:292 , PHE A:317 , TYR A:318binding site for residue Q9Z A 805
2AC2SOFTWARETRP A:553 , TRP A:564binding site for residue PGE A 806
3AC3SOFTWAREALA A:322 , ALA A:323 , ASN A:324 , ASN A:373 , TYR A:381 , HOH A:904 , HOH A:908 , HOH A:933 , HOH A:939binding site for Poly-Saccharide residues NAG A 801 through NAG A 802 bound to ASN A 373
4AC4SOFTWAREASP A:116 , TYR A:117 , LYS A:119 , SER A:547 , MET A:548 , ASN A:549 , ARG A:622binding site for Poly-Saccharide residues NAG A 803 through NAG A 804 bound to ASN A 549

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:224 -A:244
2A:415 -A:425
3A:579 -A:618
4A:601 -A:633
5A:635 -A:690
6A:642 -A:655
7A:669 -A:707

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5MRH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MRH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MRH)

(-) Exons   (0, 0)

(no "Exon" information available for 5MRH)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:639
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhheeee..eeeeeee.....eeeeeee......eeeeee.......ee...............eee.......eeee..........eeeee.......eeee.........ee.......eeee.....eeee.......eeee..eeeeee.hhh.eeeee............eeeeee.......eeeeeeeeeeeee..eeeeeee......eeeeee.......ee...........eeeeee....eeeeee......eeeeeee......eeeeeeeee..........ee.......eeeeee.....eeeeee.......eeee.................eeeeehhhhhhh.................eeeeeeee........eeeee.......eeee...eeeeeehhhheeeeee.......eeeee.......eeee......eeeeee........eeeeeee..eeeeee.........hhh.eeeee................eeeeeeee..............eeeeee...hhh.ee....ee........ee.....hhhhhhhh..ee...ee................eehhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mrh A  55 RVRDFVAKLANNTHQHVFGSVSLSWVGDSTGVILVLTTFHVPGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCLAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWTHLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQTYTFTRDPIYFTGLASEPGARSMNISIWGFTWVSYTIDFKDILERNCEEKDYTIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSMCQNGRDYVVTKQPSICLCSLEDFLCDFGYYRPENDSKCVEQPELKGHDLEFCLHLTTNGYRKIPGDKCQGGVNPVREVKDLKKKCTSNFLSPE 715
                                    64       |78        88        98 ||    114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554 ||    571       581       591       601       611       621       631       641       651       661       676       686       696       706         
                                            72|                    100|                                                                                                                                                                                                                                                                                                                                                                                                                                                              556|                                                                                                       670|                                       
                                             77                     107                                                                                                                                                                                                                                                                                                                                                                                                                                                               564                                                                                                        676
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5MRH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MRH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MRH)

(-) Gene Ontology  (50, 50)

Asymmetric/Biological Unit(hide GO term definitions)

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  5mrh
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  SORT_HUMAN | Q99523
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SORT_HUMAN | Q99523: 3f6k 3g2u 3g2v 4msl 4n7e 4po7 5mri

(-) Related Entries Specified in the PDB File

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