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(-) Description

Title :  CRYSTAL STRUCTURE OF CHICKEN NETRIN-1 (LN-LE3)
 
Authors :  K. Xu, D. B. Nikolov
Date :  18 May 14  (Deposition) - 18 Jun 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Elongated, Cysteine Rich, Glycoprotein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Xu, Z. Wu, N. Renier, A. Antipenko, D. Tzvetkova-Robev, Y. Xu, M. Minchenko, V. Nardi-Dei, K. R. Rajashankar, J. Himanen, M. Tessier-Lavigne, D. B. Nikolov
Neural Migration. Structures Of Netrin-1 Bound To Two Receptors Provide Insight Into Its Axon Guidance Mechanism.
Science V. 344 1275 2014
PubMed-ID: 24876346  |  Reference-DOI: 10.1126/SCIENCE.1255149

(-) Compounds

Molecule 1 - NETRIN-1
    ChainsA
    EngineeredYES
    Expression SystemBACULOVIRIDAE
    Expression System Taxid10442
    FragmentLN-LE3 (UNP RESIDUES 26-457)
    GeneNTN1
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3MG1Ligand/IonMAGNESIUM ION
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:109 , ASP A:112 , THR A:120 , SER A:279 , HOH A:656binding site for residue CA A 504
2AC2SOFTWAREARG A:157 , LEU A:393binding site for residue CL A 505
3AC3SOFTWAREHIS A:105 , CYS A:121 , MG A:507binding site for residue CL A 506
4AC4SOFTWAREGLN A:123 , CL A:506binding site for residue MG A 507
5AC5SOFTWAREASN A:97 , SER A:99 , HOH A:679binding site for Mono-Saccharide NAG A 501 bound to ASN A 97
6AC6SOFTWAREASN A:118binding site for Mono-Saccharide NAG A 502 bound to ASN A 118
7AC7SOFTWAREASN A:133binding site for Mono-Saccharide NAG A 503 bound to ASN A 133

(-) SS Bonds  (17, 17)

Asymmetric Unit
No.Residues
1A:43 -A:53
2A:72 -A:96
3A:80 -A:93
4A:121 -A:154
5A:183 -A:205
6A:287 -A:296
7A:289 -A:306
8A:308 -A:317
9A:320 -A:340
10A:343 -A:352
11A:345 -A:370
12A:373 -A:382
13A:385 -A:403
14A:406 -A:418
15A:408 -A:425
16A:427 -A:436
17A:439 -A:453

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Lys A:74 -Pro A:75
2Tyr A:130 -Pro A:131
3Val A:212 -Arg A:213
4Arg A:213 -Pro A:214
5Gly A:260 -Asp A:261

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLM)

(-) Sequences/Alignments

Asymmetric 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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................ee.......ee........eeeeeeeee..eeeeeeeee...hhhhh.hhhhh...........ee..........eeeeeeeeeeeeeeeeeeee......eeeeeee.......eeeeeee.hhhhhhh................ee...........eeeeee......hhhhhhhhhhhhhhheeeeeeeee.....................eeeeeeeeeee........eee.....eee.....ee.....ee..............................eeeehhhhhhhh.....eeee.....ee.....ee...eee...........eee.........................ee.....ee...eee.......eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plm A  40 PDPCYDEHGLPRRCIPDFVNSAFGKEVKVSSTCGKPPSRYCVVTEKGEEQVRSCHLCNASDPKRAHPPSFLTDLNNPHNLTCWQSDSYVQYPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGKTWVPFQFYSTQCRKMYNKPSRAAITKQNEQEAICTDSHTDVRPLSGGLIAFSTLDGRPTAHDFDNSPVLQDWVTATDIKVTFSRLHTFGDEDDSELARDSYFYAVSDLQVGGRCKCNGHASRCVRDRDDNLVCDCKHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDLSKPISHRKACKECDCHPVGAAGQTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKIP 457
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259 ||    271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      
                                                                                                                                                                                                                                                       261|                                                                                                                                                                                                 
                                                                                                                                                                                                                                                        264                                                                                                                                                                                                 

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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 4PLM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NET1_CHICK | Q909224pln 4plo

(-) Related Entries Specified in the PDB File

4pln 4plo