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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VPS10P DOMAIN OF HUMAN SORTILIN/NTS3 IN COMPLEX WITH TRIAZOLONE 18
 
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 :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Vps10P, Receptor, 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, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
3Q9Y1Ligand/Ion~{N}-METHYL-3-(3-METHYLBUTYL)-5-OXIDANYL-1,2,3-TRIAZOLE-4-CARBOXAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:102 , SER A:272 , PHE A:281 , SER A:283 , ARG A:292 , ILE A:294 , PHE A:317 , TYR A:318 , HOH A:914 , HOH A:994binding site for residue Q9Y A 807
2AC2SOFTWARELEU A:127 , ASN A:129 , PHE A:165 , GLN A:176 , HOH A:908binding site for Mono-Saccharide NAG A 806 bound to ASN A 129
3AC3SOFTWAREALA A:322 , ALA A:323 , ASN A:324 , ASN A:373 , TYR A:381 , HOH A:917 , HOH A:919 , HOH A:960 , HOH A:984 , HOH A:1153binding site for Poly-Saccharide residues NAG A 801 through BMA A 803 bound to ASN A 373
4AC4SOFTWAREASP A:116 , LYS A:119 , SER A:547 , MET A:548 , ASN A:549 , ASP A:570 , ARG A:622 , HOH A:942 , HOH A:951 , HOH A:1110 , HOH A:1146binding site for Poly-Saccharide residues NAG A 804 through NAG A 805 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 5MRI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MRI)

(-) 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:662
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.eeeee.......eeeee.......eeeeeeee..hhhhh.eeeeeeee.......ee.hhhhh..........ee.......eeeee.........eeeee.......eeee.........ee.......eeee.....eeee.......eeee..eeeeee.....eeeee............eeeeee.......eeeeeeeeeeeee..eeeeeee......eeeeee.......ee...........eeeeee....eeeeee......eeeeeee......eeeeeeeee..........ee.......eeeeee.....eeeeee.......eeee.................eeee.hhhhhhh.................eeeeeeee........eeeee.......eeee...eeeeeehhhheeeeee.......eeeee.......eeee.....eeeeeee........eeeeeeee.hhhh..eeeeeee.........hhh.eeeee................eeeeeeee..............eeeeee...hhh.eee...ee........ee....hhhhhhhhhhhhhhh.ee..eee................eehhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mri A  54 GRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIMTFGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCLAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWTHLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQTYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDYTIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSMCQNGRDYVVTKQPSICLCSLEDFLCDFGYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLKKKCTSNFLSPE 715
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (50, 50)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5mrh

(-) Related Entries Specified in the PDB File

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