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 2.08 freeze date was dated 2021-03-31, with a file datestamp of 2021-03-26.
Experiment type: XRAY
Resolution: 2.68 Å
R-factor: N/A
AEROSPACI score: 0.26 (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 2.08: 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 2.08: 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):
  • Uniprot Q0ED31 (0-79)
    • linker (80-81)
  • Uniprot Q0ED31 (82-184)
  • Uniprot Q0ED31 (191-352)
• 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 2.08: 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 2.08: 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