PDB entry 6nqd

View 6nqd on RCSB PDB site
Description: cryo-em structure of t/f100 sosip.664 hiv-1 env trimer in complex with 8anc195 fab
Deposited on 2019-01-21, released 2019-03-06
The last revision was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: EM
Resolution: 3.9 Å
R-factor: N/A
AEROSPACI score: 0.12 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: T/F100 Env gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: T/F100 Env gp41
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NQD (0-End)
    • Uniprot S6B2A6
  • Chain 'D':
    Compound: 8ANC195 G52K5 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NQD (0-End)
    • Uniprot P0DOX7
  • Chain 'E':
    Compound: T/F100 Env gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: T/F100 Env gp41
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NQD (0-End)
    • Uniprot S6B2A6
  • Chain 'H':
    Compound: 8ANC195 G52K5 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NQD (0-End)
    • Uniprot P0DOX7
  • Chain 'I':
    Compound: T/F100 Env gp120
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: T/F100 Env gp41
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
  • Chain 'K':
    Compound: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NQD (0-End)
    • Uniprot S6B2A6
  • Chain 'L':
    Compound: 8ANC195 G52K5 light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NQD (0-End)
    • Uniprot P0DOX7
  • 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:
    >6nqdA (A:)
atnnlwvtvyygvpvwrdadttlfcasdakahetevhnvwathacvptdpnpqemhlknv
tenfnmwknnmveqmqedvislwdqslkpcvkltplcvtlnctsatvtnytkvndtsdii
gnitddvrncsfnmttelrdkqqkvyalfykldivpiddssnngssnfseyrlincntsv
ikqacpkvsfdpipihyctpagyailrcndkkfngtgpcknvssvqcthgikpvvstqll
lngslaeegiiirsenltnnaktiivhfnesvkinctrpsnntrtgihigpgqvfyktgd
iigdirkaycnisgaqwhkvlgrvanklkehfnnktivfkpssggdpeitmhhfncrgef
fycnttklfnstwggnknetrdngtitipcrikqiinmwqgvgqamyappikgvikclsn
itgilltrdggndstennetfrpgggnikdnwrnelykykvvqieplgiaptkckrrvve
rrrrrr

    Sequence, based on observed residues (ATOM records):
    >6nqdA (A:)
atnnlwvtvyygvpvwrdadttlfcasdakatevhnvwathacvptdpnpqemhlknvte
nfnmwknnmveqmqedvislwdqslkpcvkltplcvtlnctsatddvrncsfnmttelrd
kqqkvyalfykldivpidnfseyrlincntsvikqacpkvsfdpipihyctpagyailrc
ndkkfngtgpcknvssvqcthgikpvvstqlllngslaeegiiirsenltnnaktiivhf
nesvkinctrpsnntrtgihigpgqvfyktgdiigdirkaycnisgaqwhkvlgrvankl
kehfnnktivfkpssggdpeitmhhfncrgeffycnttklfnstwgtrdngtitipcrik
qiinmwqgvgqamyappikgvikclsnitgilltrdggnnetfrpgggnikdnwrnelyk
ykvvqieplgiaptkckrr

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6nqdB (B:)
avglgamifgflgaagstmgaasitltvqarqllsgivqqqsnllrapeaqqhllqltvw
gikqlqarvlaverylqdqkflglwgcsgkiicctavpwnsswsnktfeeiwnnmtwiew
ereisnytsqiydiltisqtqqeknekdlleldaaawshpqfekgggsgggsggsawshp
qfek

    Sequence, based on observed residues (ATOM records):
    >6nqdB (B:)
glgamifgflgaagstmgaasitltvqarqllsgigikqlqarvlaverylqdqkflglw
gcsgkiicctavpwnsswsnktfeeiwnnmtwiewereisnytsqiydiltisqtqqekn
ekdl

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6nqdC (C:)
qihlvqsgtevkkpgssvtvsckaygvntfglyavnwvrqapgqsleyigqiwrwkssas
hhfrgrvlisavdltgssppissleiknltsddtavyfctttstydrwsglhhdgvmafs
swgqgtlisvsaastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgalts
gvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthh
hhhh

    Sequence, based on observed residues (ATOM records):
    >6nqdC (C:)
qihlvqsgtevkkpgssvtvsckaygvntfglyavnwvrqapgqsleyigqiwrwkssas
hhfrgrvlisavdltgssppissleiknltsddtavyfctttstydrwsglhhdgvmafs
swgqgtlisv

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6nqdD (D:)
diqmtqspstlsastgdtvriscrasqsitgnwvawyqqrpgkaprlliyrgaallggvp
srfrgsaagtdftltignlqaedfgtfycqqydtypgtfgqgtkvevkrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >6nqdD (D:)
diqmtqspstlsastgdtvriscrasqsitgnwvawyqqrpgkaprlliyrgaallggvp
srfrgsaagtdftltignlqaedfgtfycqqydtypgtfgqgtkvevk

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6nqdE (E:)
atnnlwvtvyygvpvwrdadttlfcasdakahetevhnvwathacvptdpnpqemhlknv
tenfnmwknnmveqmqedvislwdqslkpcvkltplcvtlnctsatvtnytkvndtsdii
gnitddvrncsfnmttelrdkqqkvyalfykldivpiddssnngssnfseyrlincntsv
ikqacpkvsfdpipihyctpagyailrcndkkfngtgpcknvssvqcthgikpvvstqll
lngslaeegiiirsenltnnaktiivhfnesvkinctrpsnntrtgihigpgqvfyktgd
iigdirkaycnisgaqwhkvlgrvanklkehfnnktivfkpssggdpeitmhhfncrgef
fycnttklfnstwggnknetrdngtitipcrikqiinmwqgvgqamyappikgvikclsn
itgilltrdggndstennetfrpgggnikdnwrnelykykvvqieplgiaptkckrrvve
rrrrrr

    Sequence, based on observed residues (ATOM records):
    >6nqdE (E:)
atnnlwvtvyygvpvwrdadttlfcasdakatevhnvwathacvptdpnpqemhlknvte
nfnmwknnmveqmqedvislwdqslkpcvkltplcvtlnctsatddvrncsfnmttelrd
kqqkvyalfykldivpidnfseyrlincntsvikqacpkvsfdpipihyctpagyailrc
ndkkfngtgpcknvssvqcthgikpvvstqlllngslaeegiiirsenltnnaktiivhf
nesvkinctrpsnntrtgihigpgqvfyktgdiigdirkaycnisgaqwhkvlgrvankl
kehfnnktivfkpssggdpeitmhhfncrgeffycnttklfnstwgtrdngtitipcrik
qiinmwqgvgqamyappikgvikclsnitgilltrdggnnetfrpgggnikdnwrnelyk
ykvvqieplgiaptkckrr

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6nqdF (F:)
avglgamifgflgaagstmgaasitltvqarqllsgivqqqsnllrapeaqqhllqltvw
gikqlqarvlaverylqdqkflglwgcsgkiicctavpwnsswsnktfeeiwnnmtwiew
ereisnytsqiydiltisqtqqeknekdlleldaaawshpqfekgggsgggsggsawshp
qfek

    Sequence, based on observed residues (ATOM records):
    >6nqdF (F:)
glgamifgflgaagstmgaasitltvqarqllsgigikqlqarvlaverylqdqkflglw
gcsgkiicctavpwnsswsnktfeeiwnnmtwiewereisnytsqiydiltisqtqqekn
ekdl

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6nqdG (G:)
qihlvqsgtevkkpgssvtvsckaygvntfglyavnwvrqapgqsleyigqiwrwkssas
hhfrgrvlisavdltgssppissleiknltsddtavyfctttstydrwsglhhdgvmafs
swgqgtlisvsaastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgalts
gvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthh
hhhh

    Sequence, based on observed residues (ATOM records):
    >6nqdG (G:)
qihlvqsgtevkkpgssvtvsckaygvntfglyavnwvrqapgqsleyigqiwrwkssas
hhfrgrvlisavdltgssppissleiknltsddtavyfctttstydrwsglhhdgvmafs
swgqgtlisv

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6nqdH (H:)
diqmtqspstlsastgdtvriscrasqsitgnwvawyqqrpgkaprlliyrgaallggvp
srfrgsaagtdftltignlqaedfgtfycqqydtypgtfgqgtkvevkrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >6nqdH (H:)
diqmtqspstlsastgdtvriscrasqsitgnwvawyqqrpgkaprlliyrgaallggvp
srfrgsaagtdftltignlqaedfgtfycqqydtypgtfgqgtkvevk

  • Chain 'I':
    Sequence, based on SEQRES records:
    >6nqdI (I:)
atnnlwvtvyygvpvwrdadttlfcasdakahetevhnvwathacvptdpnpqemhlknv
tenfnmwknnmveqmqedvislwdqslkpcvkltplcvtlnctsatvtnytkvndtsdii
gnitddvrncsfnmttelrdkqqkvyalfykldivpiddssnngssnfseyrlincntsv
ikqacpkvsfdpipihyctpagyailrcndkkfngtgpcknvssvqcthgikpvvstqll
lngslaeegiiirsenltnnaktiivhfnesvkinctrpsnntrtgihigpgqvfyktgd
iigdirkaycnisgaqwhkvlgrvanklkehfnnktivfkpssggdpeitmhhfncrgef
fycnttklfnstwggnknetrdngtitipcrikqiinmwqgvgqamyappikgvikclsn
itgilltrdggndstennetfrpgggnikdnwrnelykykvvqieplgiaptkckrrvve
rrrrrr

    Sequence, based on observed residues (ATOM records):
    >6nqdI (I:)
atnnlwvtvyygvpvwrdadttlfcasdakatevhnvwathacvptdpnpqemhlknvte
nfnmwknnmveqmqedvislwdqslkpcvkltplcvtlnctsatddvrncsfnmttelrd
kqqkvyalfykldivpidnfseyrlincntsvikqacpkvsfdpipihyctpagyailrc
ndkkfngtgpcknvssvqcthgikpvvstqlllngslaeegiiirsenltnnaktiivhf
nesvkinctrpsnntrtgihigpgqvfyktgdiigdirkaycnisgaqwhkvlgrvankl
kehfnnktivfkpssggdpeitmhhfncrgeffycnttklfnstwgtrdngtitipcrik
qiinmwqgvgqamyappikgvikclsnitgilltrdggnnetfrpgggnikdnwrnelyk
ykvvqieplgiaptkckrr

  • Chain 'J':
    Sequence, based on SEQRES records:
    >6nqdJ (J:)
avglgamifgflgaagstmgaasitltvqarqllsgivqqqsnllrapeaqqhllqltvw
gikqlqarvlaverylqdqkflglwgcsgkiicctavpwnsswsnktfeeiwnnmtwiew
ereisnytsqiydiltisqtqqeknekdlleldaaawshpqfekgggsgggsggsawshp
qfek

    Sequence, based on observed residues (ATOM records):
    >6nqdJ (J:)
glgamifgflgaagstmgaasitltvqarqllsgigikqlqarvlaverylqdqkflglw
gcsgkiicctavpwnsswsnktfeeiwnnmtwiewereisnytsqiydiltisqtqqekn
ekdl

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6nqdK (K:)
qihlvqsgtevkkpgssvtvsckaygvntfglyavnwvrqapgqsleyigqiwrwkssas
hhfrgrvlisavdltgssppissleiknltsddtavyfctttstydrwsglhhdgvmafs
swgqgtlisvsaastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgalts
gvhtfpavlqssglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthh
hhhh

    Sequence, based on observed residues (ATOM records):
    >6nqdK (K:)
qihlvqsgtevkkpgssvtvsckaygvntfglyavnwvrqapgqsleyigqiwrwkssas
hhfrgrvlisavdltgssppissleiknltsddtavyfctttstydrwsglhhdgvmafs
swgqgtlisv

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6nqdL (L:)
diqmtqspstlsastgdtvriscrasqsitgnwvawyqqrpgkaprlliyrgaallggvp
srfrgsaagtdftltignlqaedfgtfycqqydtypgtfgqgtkvevkrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >6nqdL (L:)
diqmtqspstlsastgdtvriscrasqsitgnwvawyqqrpgkaprlliyrgaallggvp
srfrgsaagtdftltignlqaedfgtfycqqydtypgtfgqgtkvevk