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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) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Coagulation Factor Domain, Discoidin Domain, Receptor, Vegf-C, Secreted, 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
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: ROSETTA-GAMI 2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PROTEOLYTIC FRAGMENT OF S9NRP2 COAGULATION FACTOR DOMAINS
    Gene: NRP2, VEGF165R2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:312BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWAREGLY A:369 , THR B:391BINDING SITE FOR RESIDUE ACT B 501

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:427 -A:277
2B:427 -B:277
3B:434 -A:434

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QDS)

(-) 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:182
                                                                                                                                                                                                                      
               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.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qds A 272 SHMFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISAS 453
                                   281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451  


Chain B from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               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.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qds B 275 FQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISAS 453
                                   284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444
   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 4QDS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  4qds
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  NRP2_HUMAN | O60462
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 Related Entries

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

UniProtKB/Swiss-Prot
        NRP2_HUMAN | O60462: 2qqj 2qqk 2qql 2qqo 4qdq 4qdr 5dn2 5dq0

(-) Related Entries Specified in the PDB File

4qdq 4qdr