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(-) Description

Title :  PHYSICAL BASIS FOR NRP2 LIGAND BINDING
 
Authors :  M. W. Parker, C. W. Vander Kooi
Date :  14 May 14  (Deposition) - 15 Apr 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Coagulation Factor Domain, Discoidin Domain, Receptor, Vegf-C, Membrane, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. W. Parker, A. D. Linkugel, H. L. Goel, T. Wu, A. M. Mercurio, C. W. Vander Kooi
Structural Basis For Vegf-C Binding To Neuropilin-2 And Sequestration By A Soluble Splice Form.
Structure V. 23 677 2015
PubMed-ID: 25752543  |  Reference-DOI: 10.1016/J.STR.2015.01.018

(-) Compounds

Molecule 1 - NEUROPILIN-2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainROSETTA-GAMI 2(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNEUROPILIN-2 B1B2 DOMAIN, VEGF-C C-TERMINUS
    GeneNRP2, VEGF165R2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)A 
Biological Unit 2 (2x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:547 , PHE A:549 , GLU A:550 , ARG A:562 , HOH A:856 , HOH A:868 , HOH A:903BINDING SITE FOR RESIDUE GOL A 701
2AC2SOFTWAREASN A:354 , GLY A:355 , HIS A:415 , ARG A:572 , HOH A:942BINDING SITE FOR RESIDUE GOL A 702
3AC3SOFTWARETRP A:372 , MET A:373 , VAL A:374 , ARG A:376 , HIS A:381 , HIS A:554 , HOH A:833 , HOH A:939BINDING SITE FOR RESIDUE GOL A 703
4AC4SOFTWAREHIS A:312 , GLN A:345 , ARG A:421 , LYS A:533BINDING SITE FOR RESIDUE SO4 A 704
5AC5SOFTWAREGLY B:355 , HIS B:415 , SER B:416BINDING SITE FOR RESIDUE GOL B 701
6AC6SOFTWARETRP B:372 , MET B:373 , VAL B:374 , ARG B:376 , HIS B:554 , HOH B:829BINDING SITE FOR RESIDUE SO4 B 702

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:427 -A:277
2A:592 -A:434
3B:427 -B:277
4B:592 -B:434

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QDQ)

(-) 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:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhh.eee.........hhhhh...................eeeeeeeeeeeeeeeee.ee......eeeeeeeeeeee......ee.ee..ee..ee........eeeeeeeeeeeeeeeeeeeeee.....eeeeeeehhhhh.............hhh.eee........hhhhhh.....................eeeeeeeeeeeeeeeee.......eeeeeeeee......ee...........ee........eeeeeeeeeeeeeeeeeeee.......eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qdq A 276 QCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVIIQGARARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWTSIIRR 600
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505 ||    524       534       544       554       564       574       584       594      
                                                                                                                                                                                                                                                                 507|                                                                                   
                                                                                                                                                                                                                                                                  517                                                                                   

Chain B from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhh.eee.........hhhhh...................eeeeeeeeeeeeeeeee.ee......eeeeeeeeeeee......ee.ee..ee..ee........eeeeeeeeeeeeeeeeeeeeee.....eeeeeeee.hhh...ee........hhh.eee........hhhhhh.....................eeeeeeeeeeeeeeeee.......eeeeeeeee......ee...........ee........eeeeeeeeeeeeeeeeeeee.......eeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qdq B 276 QCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVIIQGARARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWTSIIRR 600
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505 ||    524       534       544       554       564       574       584       594      
                                                                                                                                                                                                                                                                 507|                                                                                   
                                                                                                                                                                                                                                                                  517                                                                                   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 4QDQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NRP2_HUMAN | O604622qqj 2qqk 2qql 2qqo 4qdr 4qds 5dn2 5dq0

(-) Related Entries Specified in the PDB File

4qdr 4qds