PDB entry 6bf4

View 6bf4 on RCSB PDB site
Description: Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120
Class: viral protein/immune system
Keywords: Antibody, HIV-1, Silent face, glycan, gp120, viral protein-IMMUNE SYSTEM complex
Deposited on 2017-10-25, released 2018-03-07
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-07-09.
Experiment type: XRAY
Resolution: 2.38 Å
R-factor: N/A
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: HIV-1 clade AE gp120 core
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • PDB 6BF4 (0-343)
  • Chain 'B':
    Compound: VRC-PG05 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6BF4 (0-End)
    Domains in SCOPe 2.08: d6bf4b_
  • Chain 'C':
    Compound: VRC-PG05 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6BF4 (0-218)
    Domains in SCOPe 2.08: d6bf4c1, d6bf4c2
  • Chain 'G':
    Compound: HIV-1 clade AE gp120 core
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • PDB 6BF4 (0-End)
  • Chain 'H':
    Compound: VRC-PG05 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6BF4 (0-End)
    Domains in SCOPe 2.08: d6bf4h_
  • Chain 'L':
    Compound: VRC-PG05 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6BF4 (0-End)
    Domains in SCOPe 2.08: d6bf4l1, d6bf4l2
  • Heterogens: NAG, EDO, ACT, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6bf4B (B:)
evqlvesggglvqpggslrlscaasgfpfnrdwmtwvrqapgkglewvaninmdgdkkdy
vdsvkgrftisrdnaktslylqmnslragdtavyycarirqvskylqwypgvfemwgqgt
mvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfp
avlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

    Sequence, based on observed residues (ATOM records): (download) 
    >6bf4B (B:)
evqlvesggglvqpggslrlscaasgfpfnrdwmtwvrqapgkglewvaninmdgdkkdy
vdsvkgrftisrdnaktslylqmnslragdtavyycarirqvskylqwypgvfemwgqgt
mvtvssastkgpsvfplapsstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpav
lqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >6bf4C (C:)
divmtqspdslavslgeratihckssqsvlyrpnnrnyvawyqqkpgqpprllihwasfr
esgvpdrftgsgsgtdftltisslqaedvavyycqqyfflysfgggtkleinrtvaapsv
fifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysl
sstltlskadyekhkvyacevthqglsspvtksfnrgec

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >6bf4H (H:)
evqlvesggglvqpggslrlscaasgfpfnrdwmtwvrqapgkglewvaninmdgdkkdy
vdsvkgrftisrdnaktslylqmnslragdtavyycarirqvskylqwypgvfemwgqgt
mvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfp
avlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

    Sequence, based on observed residues (ATOM records): (download) 
    >6bf4H (H:)
evqlvesggglvqpggslrlscaasgfpfnrdwmtwvrqapgkglewvaninmdgdkkdy
vdsvkgrftisrdnaktslylqmnslragdtavyycarirqvskylqwypgvfemwgqgt
mvtvssastkgpsvfplapssgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvep

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >6bf4L (L:)
divmtqspdslavslgeratihckssqsvlyrpnnrnyvawyqqkpgqpprllihwasfr
esgvpdrftgsgsgtdftltisslqaedvavyycqqyfflysfgggtkleinrtvaapsv
fifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysl
sstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >6bf4L (L:)
divmtqspdslavslgeratihckssqsvlyrpnnrnyvawyqqkpgqpprllihwasfr
esgvpdrftgsgsgtdftltisslqaedvavyycqqyfflysfgggtkleinrtvaapsv
fifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysl
sstltlskadyekhkvyacevthqglsspvtksfnrge