PDB entry 5if0

View 5if0 on RCSB PDB site
Description: Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor in complex with with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.44 A
Class: immune system/viral protein
Keywords: HIV-1 gp120, engineered outer domain (eOD), germline targeting, CD4 binding site, VRC01-class naive human germline antibody, immune system, viral-protein complex, IMMUNE SYSTEM-VIRAL PROTEIN complex
Deposited on 2016-02-25, released 2016-04-06
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-04-06, with a file datestamp of 2016-04-01.
Experiment type: XRAY
Resolution: 2.44 Å
R-factor: N/A
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: VRC01cHuGL2 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5IF0 (0-End)
  • Chain 'B':
    Compound: VRC01c-HuGL2 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5IF0 (0-End)
    Domains in SCOPe 2.07: d5if0b1, d5if0b2
  • Chain 'G':
    Compound: Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5IF0 (0-End)
  • Chain 'H':
    Compound: VRC01cHuGL2 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5IF0 (0-End)
  • Chain 'I':
    Compound: Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5IF0 (0-End)
  • Chain 'L':
    Compound: VRC01c-HuGL2 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 5IF0 (0-End)
    Domains in SCOPe 2.07: d5if0l1, d5if0l2
  • Heterogens: NAG, PO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5if0B (B:)
    divmtqspdslavslgeratinckssqsvlyssnnknylawyqqkpgqppklliywastr
    esgvpdrfsgsgsgtdftltisslqaedvavyycqqyysfgggtkveikrtvaapsvfif
    ppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsst
    ltlskadyekhkvyacevthqglrspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >5if0B (B:)
    divmtqspdslavslgeratinckssqknylawyqqkpgqppklliywastresgvpdrf
    sgsgsgtdftltisslqaedvavyycqqyysfgggtkveikrtvaapsvfifppsdeqlk
    sgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltlskady
    ekhkvyacevthqglrspvtksfnrg
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >5if0L (L:)
    divmtqspdslavslgeratinckssqsvlyssnnknylawyqqkpgqppklliywastr
    esgvpdrfsgsgsgtdftltisslqaedvavyycqqyysfgggtkveikrtvaapsvfif
    ppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsst
    ltlskadyekhkvyacevthqglrspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >5if0L (L:)
    divmtqspdslavslgeratinckssqknylawyqqkpgqppklliywastresgvpdrf
    sgsgsgtdftltisslqaedvavyycqqyysfgggtkveikrtvaapsvfifppsdeqlk
    sgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltlskady
    ekhkvyacevthqglrspvtksfnrg