PDB entry 5vyp

View 5vyp on RCSB PDB site
Description: Crystal structure of the Plant Defensin NsD7 bound to PIP2
Class: antimicrobial protein
Keywords: antimicrobial, antifungal, defensin, ANTIMICROBIAL PROTEIN
Deposited on 2017-05-25, released 2017-08-02
The last revision prior to the SCOPe 2.06 freeze date was dated 2017-08-02, with a file datestamp of 2017-07-28.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: N/A
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5vypa_
  • Chain 'B':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypb1, d5vypb2
  • Chain 'C':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypc1, d5vypc2
  • Chain 'D':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypd1, d5vypd2
  • Chain 'E':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vype1, d5vype2
  • Chain 'F':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypf1, d5vypf2
  • Chain 'G':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypg1, d5vypg2
  • Chain 'H':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vyph1, d5vyph2
  • Chain 'I':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypi1, d5vypi2
  • Chain 'J':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypj1, d5vypj2
  • Chain 'K':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-End)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypk1, d5vypk2
  • Chain 'L':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5vypl_
  • Chain 'M':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5vypm_
  • Chain 'N':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5vypn_
  • Chain 'O':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypo1, d5vypo2
  • Chain 'P':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypp1, d5vypp2
  • Chain 'Q':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypq1, d5vypq2
  • Chain 'R':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypr1, d5vypr2
  • Chain 'S':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vyps1, d5vyps2
  • Chain 'T':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypt1, d5vypt2
  • Chain 'U':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypu1, d5vypu2
  • Chain 'V':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypv1, d5vypv2
  • Chain 'W':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypw1, d5vypw2
  • Chain 'X':
    Compound: Defensin NsD7
    Species: Nicotiana suaveolens [TaxId:200320]
    Database cross-references and differences (RAF-indexed):
    • Uniprot C0HK49 (1-47)
      • expression tag (0)
    Domains in SCOPe 2.06: d5vypx1, d5vypx2
  • Heterogens: PIO, SO4, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5vypA (A:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

    Sequence, based on observed residues (ATOM records): (download) 
    >5vypA (A:)
kdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypB (B:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypC (C:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypD (D:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypE (E:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypF (F:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypG (G:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypH (H:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypI (I:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypJ (J:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >5vypK (K:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

    Sequence, based on observed residues (ATOM records): (download) 
    >5vypK (K:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkp

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >5vypL (L:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

    Sequence, based on observed residues (ATOM records): (download) 
    >5vypL (L:)
dckresntfpgicitkppcrkacirekftdghcskilrrclctkp

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >5vypM (M:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

    Sequence, based on observed residues (ATOM records): (download) 
    >5vypM (M:)
kdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >5vypN (N:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

    Sequence, based on observed residues (ATOM records): (download) 
    >5vypN (N:)
kdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypO (O:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypP (P:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypQ (Q:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypR (R:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypS (S:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'T':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypT (T:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'U':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypU (U:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypV (V:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypW (W:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5vypX (X:)
akdckresntfpgicitkppcrkacirekftdghcskilrrclctkpc