PDB entry 6vlr

View 6vlr on RCSB PDB site
Description: bg505 sosip.v5.2 in complex with rhesus macaque fab rm20e1 and pgt122 fab
Deposited on 2020-01-24, released 2020-06-24
The last revision was dated 2020-09-16, with a file datestamp of 2020-09-11.
Experiment type: EM
Resolution: 4.42 Å
R-factor: N/A
AEROSPACI score: 0.14 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: envelope glycoprotein gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S6
      • conflict (42)
      • conflict (283)
      • conflict (300)
      • conflict (468)
  • Chain 'B':
    Compound: BG505 SOSIPv5.2 gp41
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S6
      • conflict (93)
  • Chain 'C':
    Compound: PGT122 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VLR (0-131)
  • Chain 'D':
    Compound: PGT122 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VLR (0-131)
  • Chain 'E':
    Compound: PGT122 Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VLR (0-131)
  • Chain 'F':
    Compound: RM20E1 Fab Heavy Chain
    Species: MACACA MULATTA [TaxId:9544]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VLR (0-122)
  • Chain 'G':
    Compound: envelope glycoprotein gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S6
      • conflict (42)
      • conflict (283)
      • conflict (300)
      • conflict (468)
  • Chain 'H':
    Compound: envelope glycoprotein gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S6
      • conflict (42)
      • conflict (283)
      • conflict (300)
      • conflict (468)
  • Chain 'I':
    Compound: BG505 SOSIPv5.2 gp41
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S6
      • conflict (93)
  • Chain 'J':
    Compound: BG505 SOSIPv5.2 gp41
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q2N0S6
      • conflict (93)
  • Chain 'K':
    Compound: PGT122 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VLR (0-105)
  • Chain 'L':
    Compound: PGT122 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VLR (0-105)
  • Chain 'M':
    Compound: PGT122 Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VLR (0-105)
  • Chain 'N':
    Compound: RM20E1 Fab Kappa Chain
    Species: MACACA MULATTA [TaxId:9544]
    Database cross-references and differences (RAF-indexed):
    • PDB 6VLR (0-111)
  • Heterogens: NAG

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6vlrA (A:)
aenlwvtvyygvpvwkdaettlfcasdakayetkkhnvwathccvptdpnpqeihlenvt
eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtnnitddmrgelkncs
fnmttelrdkkqkvyslfyrldvvqinenqgnrsnnsnkeyrlincntsaitqacpkvsf
epipihycapagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeev
mirsenitnnaknilvqfntpvqinctrpnnntrksirigpgqwfyatgdiigdirqahc
nvskatwnetlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglf
nstwisntsvqgsnstgsndsitlpcrikqiinmwqrigqamyappiqgvircvsnitgl
iltrdggstnsttetfrpgggdmrdnwrselykykvvkieplgvaptrckrrvvg

    Sequence, based on observed residues (ATOM records):
    >6vlrA (A:)
wvtvyygvpvwkdaettlfcasdanvwathccvptdpnpqeihlenvteefnmwknnmve
qmhtdiislwdqslkpcvkltplcvtlqctnvtnnigelkncsfnmttelrdkkqkvysl
fyrldvvqinenkeyrlincntsaitqacpkvsfepipihycapagfailkckdkkfngt
gpcpsvstvqcthgikpvvstqlllngslaeeevmirsenitnnaknilvqfntpvqinc
trpnnntrksirigpgqwfyatgdiigdirqahcnvskatwnetlgkvvkqlrkhfgnnt
iirfanssggdlevtthsfncggeffycntsglfnstwisnndsitlpcrikqiinmwqr
igqamyappiqgvircvsnitgliltrdgsttetfrpgggdmrdnwrselykykvvkiep
lgvaptrckr

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6vlrB (B:)
avgigavflgflgaagstmgaasmtltvqarnllsgivqqqsnllrapecqqhllkltvw
gikqlqarvlaverylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqw
dkeisnytqiiyglleesqnqqekneqdllald

    Sequence, based on observed residues (ATOM records):
    >6vlrB (B:)
igavflgflgaagstmgaasmtltvqarnllsltvwgikqlqarvlaverylrdqqllgi
wgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnqqek
neqdllal

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >6vlrC (C:)
qvhlqesgpglvkpsetlsltcnvsgtlvrdnywswirqplgkqpewigyvhdsgdtnyn
pslksrvhlsldksknlvslrltgvtaadsaiyycattkhgrriygvvafkewftyfymd
vwgkgtsvtvss

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >6vlrD (D:)
qvhlqesgpglvkpsetlsltcnvsgtlvrdnywswirqplgkqpewigyvhdsgdtnyn
pslksrvhlsldksknlvslrltgvtaadsaiyycattkhgrriygvvafkewftyfymd
vwgkgtsvtvss

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >6vlrE (E:)
qvhlqesgpglvkpsetlsltcnvsgtlvrdnywswirqplgkqpewigyvhdsgdtnyn
pslksrvhlsldksknlvslrltgvtaadsaiyycattkhgrriygvvafkewftyfymd
vwgkgtsvtvss

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >6vlrF (F:)
evqlvqseaevkrpgeslkiscqtsgynfpnywitwvrqmpgkglewmgtidprdsdtky
spsfqgqvtisadksintaylqwtslrasdsatyycvmwvyilttgniwvdvwgpgvlvt
vss

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6vlrG (G:)
aenlwvtvyygvpvwkdaettlfcasdakayetkkhnvwathccvptdpnpqeihlenvt
eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtnnitddmrgelkncs
fnmttelrdkkqkvyslfyrldvvqinenqgnrsnnsnkeyrlincntsaitqacpkvsf
epipihycapagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeev
mirsenitnnaknilvqfntpvqinctrpnnntrksirigpgqwfyatgdiigdirqahc
nvskatwnetlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglf
nstwisntsvqgsnstgsndsitlpcrikqiinmwqrigqamyappiqgvircvsnitgl
iltrdggstnsttetfrpgggdmrdnwrselykykvvkieplgvaptrckrrvvg

    Sequence, based on observed residues (ATOM records):
    >6vlrG (G:)
wvtvyygvpvwkdaettlfcasdanvwathccvptdpnpqeihlenvteefnmwknnmve
qmhtdiislwdqslkpcvkltplcvtlqctnvtnnigelkncsfnmttelrdkkqkvysl
fyrldvvqinenkeyrlincntsaitqacpkvsfepipihycapagfailkckdkkfngt
gpcpsvstvqcthgikpvvstqlllngslaeeevmirsenitnnaknilvqfntpvqinc
trpnnntrksirigpgqwfyatgdiigdirqahcnvskatwnetlgkvvkqlrkhfgnnt
iirfanssggdlevtthsfncggeffycntsglfnstwisnndsitlpcrikqiinmwqr
igqamyappiqgvircvsnitgliltrdgsttetfrpgggdmrdnwrselykykvvkiep
lgvaptrckr

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6vlrH (H:)
aenlwvtvyygvpvwkdaettlfcasdakayetkkhnvwathccvptdpnpqeihlenvt
eefnmwknnmveqmhtdiislwdqslkpcvkltplcvtlqctnvtnnitddmrgelkncs
fnmttelrdkkqkvyslfyrldvvqinenqgnrsnnsnkeyrlincntsaitqacpkvsf
epipihycapagfailkckdkkfngtgpcpsvstvqcthgikpvvstqlllngslaeeev
mirsenitnnaknilvqfntpvqinctrpnnntrksirigpgqwfyatgdiigdirqahc
nvskatwnetlgkvvkqlrkhfgnntiirfanssggdlevtthsfncggeffycntsglf
nstwisntsvqgsnstgsndsitlpcrikqiinmwqrigqamyappiqgvircvsnitgl
iltrdggstnsttetfrpgggdmrdnwrselykykvvkieplgvaptrckrrvvg

    Sequence, based on observed residues (ATOM records):
    >6vlrH (H:)
wvtvyygvpvwkdaettlfcasdanvwathccvptdpnpqeihlenvteefnmwknnmve
qmhtdiislwdqslkpcvkltplcvtlqctnvtnnigelkncsfnmttelrdkkqkvysl
fyrldvvqinenkeyrlincntsaitqacpkvsfepipihycapagfailkckdkkfngt
gpcpsvstvqcthgikpvvstqlllngslaeeevmirsenitnnaknilvqfntpvqinc
trpnnntrksirigpgqwfyatgdiigdirqahcnvskatwnetlgkvvkqlrkhfgnnt
iirfanssggdlevtthsfncggeffycntsglfnstwisnndsitlpcrikqiinmwqr
igqamyappiqgvircvsnitgliltrdgsttetfrpgggdmrdnwrselykykvvkiep
lgvaptrckr

  • Chain 'I':
    Sequence, based on SEQRES records:
    >6vlrI (I:)
avgigavflgflgaagstmgaasmtltvqarnllsgivqqqsnllrapecqqhllkltvw
gikqlqarvlaverylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqw
dkeisnytqiiyglleesqnqqekneqdllald

    Sequence, based on observed residues (ATOM records):
    >6vlrI (I:)
gflgaagstmgaasmtltvqarnllsltvwgikqlqarvlaverylrdqqllgiwgcsgk
licctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnqqekneqdll
al

  • Chain 'J':
    Sequence, based on SEQRES records:
    >6vlrJ (J:)
avgigavflgflgaagstmgaasmtltvqarnllsgivqqqsnllrapecqqhllkltvw
gikqlqarvlaverylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqw
dkeisnytqiiyglleesqnqqekneqdllald

    Sequence, based on observed residues (ATOM records):
    >6vlrJ (J:)
gflgaagstmgaasmtltvqarnllsltvwgikqlqarvlaverylrdqqllgiwgcsgk
licctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnqqekneqdll
al

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records:
    >6vlrK (K:)
tfvsvapgqtaritcgeeslgsrsviwyqqrpgqapsliiynnndrpsgipdrfsgspgs
tfgttatltitsveagdeadyychiwdsrrptnwvfgegttlivls

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records:
    >6vlrL (L:)
tfvsvapgqtaritcgeeslgsrsviwyqqrpgqapsliiynnndrpsgipdrfsgspgs
tfgttatltitsveagdeadyychiwdsrrptnwvfgegttlivls

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records:
    >6vlrM (M:)
tfvsvapgqtaritcgeeslgsrsviwyqqrpgqapsliiynnndrpsgipdrfsgspgs
tfgttatltitsveagdeadyychiwdsrrptnwvfgegttlivls

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records:
    >6vlrN (N:)
dvvmtqsplslpitpgqpasiscrssqslvhnngntyltwyqqrpgqpprrliyqvsnrd
sgvpdrfigsgagtdftlkisrvesedvgiyycgqitdfpysfgqgtkvdik