PDB entry 3ngb

View 3ngb on RCSB PDB site
Description: Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120
Class: viral protein/immune system
Keywords: HIV, gp120, antibody, VRC01, neutralization, vaccine, envelope glycoprotein, VIRAL PROTEIN-IMMUNE SYSTEM complex
Deposited on 2010-06-11, released 2010-07-07
The last revision prior to the SCOPe 2.06 freeze date was dated 2010-09-01, with a file datestamp of 2010-08-27.
Experiment type: XRAY
Resolution: 2.68 Å
R-factor: 0.2
AEROSPACI score: 0.31 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: envelope glycoprotein gp160
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: Env, pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q0ED31 (0-79)
      • linker (80-81)
    • Uniprot Q0ED31 (82-184)
      • linker (189-190)
    • Uniprot Q0ED31 (191-352)
  • Chain 'B':
    Compound: Antigen binding fragment of heavy chain: Antibody VRC01
    Species: Homo sapiens [TaxId:9606]
    Gene: Heavy chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3NGB (0-223)
  • Chain 'C':
    Compound: Antigen binding fragment of light chain: Antibody VRC01
    Species: Homo sapiens [TaxId:9606]
    Gene: Light chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3NGB (0-209)
    Domains in SCOPe 2.06: d3ngbc1, d3ngbc2
  • Chain 'D':
    Compound: envelope glycoprotein gp160
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: Env, pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q0ED31 (0-79)
      • linker (80-81)
    • Uniprot Q0ED31 (82-184)
      • linker (188-190)
    • Uniprot Q0ED31 (191-352)
  • Chain 'E':
    Compound: Antigen binding fragment of heavy chain: Antibody VRC01
    Species: Homo sapiens [TaxId:9606]
    Gene: Heavy chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3NGB (0-223)
  • Chain 'F':
    Compound: Antigen binding fragment of light chain: Antibody VRC01
    Species: Homo sapiens [TaxId:9606]
    Gene: Light chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3NGB (Start-209)
    Domains in SCOPe 2.06: d3ngbf1, d3ngbf2
  • Chain 'G':
    Compound: envelope glycoprotein gp160
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: Env, pol
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Antigen binding fragment of heavy chain: Antibody VRC01
    Species: Homo sapiens [TaxId:9606]
    Gene: Heavy chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3NGB (0-223)
  • Chain 'I':
    Compound: envelope glycoprotein gp160
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: Env, pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q0ED31 (0-79)
      • linker (80-81)
    • Uniprot Q0ED31 (82-184)
      • linker (190)
      • linker (185)
    • Uniprot Q0ED31 (191-352)
  • Chain 'J':
    Compound: Antigen binding fragment of heavy chain: Antibody VRC01
    Species: Homo sapiens [TaxId:9606]
    Gene: Heavy chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3NGB (0-223)
  • Chain 'K':
    Compound: Antigen binding fragment of light chain: Antibody VRC01
    Species: Homo sapiens [TaxId:9606]
    Gene: Light chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3NGB (0-209)
    Domains in SCOPe 2.06: d3ngbk1, d3ngbk2
  • Chain 'L':
    Compound: Antigen binding fragment of light chain: Antibody VRC01
    Species: Homo sapiens [TaxId:9606]
    Gene: Light chain
    Database cross-references and differences (RAF-indexed):
    • PDB 3NGB (Start-209)
    Domains in SCOPe 2.06: d3ngbl1, d3ngbl2
  • Heterogens: NAG, BGC, TRS, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3ngbC (C:)
    eivltqspgtlslspgetaiiscrtsqygslawyqqrpgqaprlviysgstraagipdrf
    sgsrwgpdynltisnlesgdfgvyycqqyeffgqgtkvqvdikrtvaapsvfifppsdeq
    lksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltlska
    dyekhkvyacevthqglrspvtksfnrgec
    

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3ngbF (F:)
    eivltqspgtlslspgetaiiscrtsqygslawyqqrpgqaprlviysgstraagipdrf
    sgsrwgpdynltisnlesgdfgvyycqqyeffgqgtkvqvdikrtvaapsvfifppsdeq
    lksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltlska
    dyekhkvyacevthqglrspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ngbF (F:)
    vltqspgtlslspgetaiiscrtsqygslawyqqrpgqaprlviysgstraagipdrfsg
    srwgpdynltisnlesgdfgvyycqqyeffgqgtkvqvdikrtvaapsvfifppsdeqlk
    sgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltlskady
    ekhkvyacevthqglrspvtksfnrgec
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3ngbK (K:)
    eivltqspgtlslspgetaiiscrtsqygslawyqqrpgqaprlviysgstraagipdrf
    sgsrwgpdynltisnlesgdfgvyycqqyeffgqgtkvqvdikrtvaapsvfifppsdeq
    lksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltlska
    dyekhkvyacevthqglrspvtksfnrgec
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >3ngbL (L:)
    eivltqspgtlslspgetaiiscrtsqygslawyqqrpgqaprlviysgstraagipdrf
    sgsrwgpdynltisnlesgdfgvyycqqyeffgqgtkvqvdikrtvaapsvfifppsdeq
    lksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltlska
    dyekhkvyacevthqglrspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >3ngbL (L:)
    vltqspgtlslspgetaiiscrtsqygslawyqqrpgqaprlviysgstraagipdrfsg
    srwgpdynltisnlesgdfgvyycqqyeffgqgtkvqvdikrtvaapsvfifppsdeqlk
    sgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstltlskady
    ekhkvyacevthqglrspvtksfnrgec