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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VPS10P DOMAIN OF HUMAN SORTILIN/NTS3 IN COMPLEX WITH AF40431
 
Authors :  J. L. Andersen, D. Strandbygaard, S. Thirup
Date :  18 Sep 13  (Deposition) - 12 Feb 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Prongf, Alzheimer'S Disease, Beta-Propeller, Asp-Box Repeat, Vps10P Domain, 10Cc Domain, Receptor Sorting, Peptide Binding, Protein Binding, Membrane, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Andersen, T. J. Schrder, S. Christensen, D. Strandbygard, L. T. Pallesen, M. M. Garcia-Alai, S. Lindberg, M. Langgard, J. C. Eskildsen, L. David, L. Tagmose, K. B. Simonsen, P. J. Maltas, L. C. Rnn, I. E. De Jong, I. J. Malik, J. Egebjerg, J. J. Karlsson, S. Uppalanchi, D. R. Sakumudi, P. Eradi, S. P. Watson, S. Thirup
Identification Of The First Small-Molecule Ligand Of The Neuronal Receptor Sortilin And Structure Determination Of The Receptor-Ligand Complex.
Acta Crystallogr. , Sect. D V. 70 451 2014
PubMed-ID: 24531479  |  Reference-DOI: 10.1107/S1399004713030149

(-) Compounds

Molecule 1 - SORTILIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: HUMAN EMBRYONIC KIDNEY 293F CELLS
    Expression System Plasmid: PCEP-PU
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: VPS10P DOMAIN (UNP RESIDUES 78-756)
    Gene: SORT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 100 KDA NT RECEPTOR, GLYCOPROTEIN 95, GP95, NEUROTENSIN RECEPTOR 3, NT3, NTR3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
12ET1Ligand/IonN-[(7-HYDROXY-4-METHYL-2-OXO-2H-CHROMEN-8-YL)METHYL]-L-LEUCINE
2BMA2Ligand/IonBETA-D-MANNOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:79 , THR A:537 , LEU A:539 , TRP A:553 , TRP A:564BINDING SITE FOR RESIDUE PG4 A 808
2AC2SOFTWARETYR A:271 , PHE A:273 , SER A:283 , ARG A:292 , PHE A:317 , TYR A:318 , SER A:319BINDING SITE FOR RESIDUE 2ET A 809
3AC3SOFTWAREALA A:322 , ALA A:323 , ASN A:324 , ASN A:373 , THR A:375 , TYR A:381 , HOH A:908 , HOH A:910BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 373 RESIDUES 801 TO 804
4AC4SOFTWAREASP A:116 , LYS A:119 , SER A:547 , MET A:548 , ASN A:549 , ASP A:570 , ARG A:622BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 549 RESIDUES 805 TO 807

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:53 -A:523
2A:224 -A:244
3A:415 -A:425
4A:579 -A:618
5A:601 -A:633
6A:635 -A:690
7A:642 -A:655
8A:669 -A:707

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MSL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MSL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MSL)

(-) Exons   (0, 0)

(no "Exon" information available for 4MSL)

(-) 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    
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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:654
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhh.eeeee.......eeeeee.....eeeeeee.....eeeeee.......ee.hhhhh....hhhh.eee.......eeeee.........eeeee.......eeee.........ee.......eeee.....eeee.......eeee....eeee.....eeeee............eeeeee.......eeeeeeeeeeeee..eeeeeee......eeeeee.......ee...........eeeeeee..eeeeeee......eeeeeee......eeeeeeeee..........ee.......eeeeee.....eeeeee.......ee...................eeee.hhhhhhh.................eeeeeeee........eeeee.......eeee...eeeeeehhhheeeeee.......eeeee.......eeee......eeeeeee.......eeeeeee......eeeeeee.........hhh.eeeee................eeeeeeee...............eeeee.eehhh.eee...ee........ee....hhhhhhhhhhhhhhhhee..eee......eee.......eehhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4msl A  53 CGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCLAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWTHLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQTYTFTRDPIYFTGLASEPGARSMNISIWGFTESTSQWVSYTIDFKDILERNCEEKDYTIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSMCQNGRDYVVTKQPSICLCSLEDFLCDFGYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLKKKCTSNFLSPE 715
                                    62        72        82        92      |109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711    
                                                                         99|                                                                                                                                                                                                                                                                                                                                                                                                                                                                558|                                                                                                                                                          
                                                                         107                                                                                                                                                                                                                                                                                                                                                                                                                                                                 561
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4MSL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MSL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MSL)

(-) 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 4n7e 4po7 5mrh 5mri

(-) Related Entries Specified in the PDB File

3f6k