PDB entry 6myy

View 6myy on RCSB PDB site
Description: germline vrc01 antibody recognition of a modified clade c hiv-1 envelope trimer, 3 fabs bound, sharpened map
Deposited on 2018-11-02, released 2018-11-14
The last revision was dated 2020-07-29, with a file datestamp of 2020-07-09.
Experiment type: EM
Resolution: 3.8 Å
R-factor: N/A
AEROSPACI score: 0.17 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 426c DS-SOSIP D3
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MYY
  • Chain 'B':
    Compound: 426c DS-SOSIP D3
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MYY
  • Chain 'C':
    Compound: VRC01GL light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: VRC01GL heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MYY (0-109)
    • Uniprot S6C4S0 (110-End)
  • Chain 'E':
    Compound: 426c DS-SOSIP D3
    Species: HUMAN IMMUNODEFICIENCY VIRUS 1 [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MYY
  • Chain 'F':
    Compound: VRC01GL light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: VRC01GL heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MYY (0-109)
    • Uniprot S6C4S0 (110-End)
  • Chain 'H':
    Compound: VRC01GL heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MYY (0-109)
    • Uniprot S6C4S0 (110-End)
  • Chain 'L':
    Compound: VRC01GL light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
  • 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:
    >6myyA (A:)
aenlwvtvyygvpvwkeakttlfcasdakayekevhnvwathacvptdpnpqevvlenvt
enfnmwkndmvdqmqedvisiwdqslkpcvkltplcvtlnctnvnvtsnstnvnssstdn
ttlgeikncsfditteirdktrkeyalfyrldivpldnssnpnssntyrlincntstctq
acpkvtfdpipihycapagyailkcnnktfngkgpcnnvstvqcthgikpvvstqlllng
slaeeeivirsknladnakiiivqlnksveivctrpnnntrrsirigpgqtfyatdiigd
irqaycnisgrnwseavnqvkkklkehfphknisfqsssggdleitthsfncggeffycn
tsglfndtisnatimlpcrikqiinmwqevgkciyappikgnitcksditgllllrdgcn
tannaeifrpgggdmrdnwrselykykvvkieplgvaptrckrrvvgrrrrrravgigav
flgflgaagstmgaasmtltvqarnllsgivqqqsnllrapeaqqhllkltvwgikqlqa
rvlaverylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisny
tqiiyglleesqnqqekneqdllald

    Sequence, based on observed residues (ATOM records):
    >6myyA (A:)
nlwvtvyygvpvwkeakttlfcashnvwathacvptdpnpqevvlenvtenfnmwkndmv
dqmqedvisiwdqslkpcvkltplcvtlnctnvtlgeikncsfditteirdktrkeyalf
yrldivplsntyrlincntstctqacpkvtfdpipihycapagyailkcnnktfngkgpc
nnvstvqcthgikpvvstqlllngslaeeeivirsknladnakiiivqlnksveivctrp
nnntrrsirigpgqtfyatdiigdirqaycnisgrnwseavnqvkkklkehfphknisfq
sssggdleitthsfncggeffycntsglfndtisnatimlpcrikqiinmwqevgkciya
ppikgnitcksditgllllrdgcntannaeifrpgggdmrdnwrselykykvvkieplgv
aptrckrrflgaagstmgaasmtltvqarnllsgivvwgikqlqarvlaverylrdqqll
giwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnqq
ekneqdllal

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6myyB (B:)
aenlwvtvyygvpvwkeakttlfcasdakayekevhnvwathacvptdpnpqevvlenvt
enfnmwkndmvdqmqedvisiwdqslkpcvkltplcvtlnctnvnvtsnstnvnssstdn
ttlgeikncsfditteirdktrkeyalfyrldivpldnssnpnssntyrlincntstctq
acpkvtfdpipihycapagyailkcnnktfngkgpcnnvstvqcthgikpvvstqlllng
slaeeeivirsknladnakiiivqlnksveivctrpnnntrrsirigpgqtfyatdiigd
irqaycnisgrnwseavnqvkkklkehfphknisfqsssggdleitthsfncggeffycn
tsglfndtisnatimlpcrikqiinmwqevgkciyappikgnitcksditgllllrdgcn
tannaeifrpgggdmrdnwrselykykvvkieplgvaptrckrrvvgrrrrrravgigav
flgflgaagstmgaasmtltvqarnllsgivqqqsnllrapeaqqhllkltvwgikqlqa
rvlaverylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisny
tqiiyglleesqnqqekneqdllald

    Sequence, based on observed residues (ATOM records):
    >6myyB (B:)
nlwvtvyygvpvwkeakttlfcashnvwathacvptdpnpqevvlenvtenfnmwkndmv
dqmqedvisiwdqslkpcvkltplcvtlnctnvtlgeikncsfditteirdktrkeyalf
yrldivplsntyrlincntstctqacpkvtfdpipihycapagyailkcnnktfngkgpc
nnvstvqcthgikpvvstqlllngslaeeeivirsknladnakiiivqlnksveivctrp
nnntrrsirigpgqtfyatdiigdirqaycnisgrnwseavnqvkkklkehfphknisfq
sssggdleitthsfncggeffycntsglfndtisnatimlpcrikqiinmwqevgkciya
ppikgnitcksditgllllrdgcntannaeifrpgggdmrdnwrselykykvvkieplgv
aptrckrrflgaagstmgaasmtltvqarnllsgivvwgikqlqarvlaverylrdqqll
giwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnqq
ekneqdllal

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6myyC (C:)
mgwsciilflvatatgvhseivltqspatlslspgeratlscrasqsvssylawyqqkpg
qaprlliydasnratgiparfsgsgsgtdftltisslepedfavyycqqyeffgqgtkle
ikrtvaapsvfifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvte
qdskdstyslsstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >6myyC (C:)
eivltqspatlslspgeratlscrasqsvssylawyqqkpgqaprlliydasnratgipa
rfsgsgsgtdftltisslepedfavyycqqyeffgqgtkl

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6myyD (D:)
evqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwinpnsggtny
cqkfqgrvtmtrdtsistaymelsrlrsddtavyycargknsdynwdfqhwgqgtlvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthhhhhh

    Sequence, based on observed residues (ATOM records):
    >6myyD (D:)
evqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwinpnsggtny
cqkfqgrvtmtrdtsistaymelsrlrsddtavyycargknsdynwdfqhwgqgtlvtv

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6myyE (E:)
aenlwvtvyygvpvwkeakttlfcasdakayekevhnvwathacvptdpnpqevvlenvt
enfnmwkndmvdqmqedvisiwdqslkpcvkltplcvtlnctnvnvtsnstnvnssstdn
ttlgeikncsfditteirdktrkeyalfyrldivpldnssnpnssntyrlincntstctq
acpkvtfdpipihycapagyailkcnnktfngkgpcnnvstvqcthgikpvvstqlllng
slaeeeivirsknladnakiiivqlnksveivctrpnnntrrsirigpgqtfyatdiigd
irqaycnisgrnwseavnqvkkklkehfphknisfqsssggdleitthsfncggeffycn
tsglfndtisnatimlpcrikqiinmwqevgkciyappikgnitcksditgllllrdgcn
tannaeifrpgggdmrdnwrselykykvvkieplgvaptrckrrvvgrrrrrravgigav
flgflgaagstmgaasmtltvqarnllsgivqqqsnllrapeaqqhllkltvwgikqlqa
rvlaverylrdqqllgiwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisny
tqiiyglleesqnqqekneqdllald

    Sequence, based on observed residues (ATOM records):
    >6myyE (E:)
nlwvtvyygvpvwkeakttlfcashnvwathacvptdpnpqevvlenvtenfnmwkndmv
dqmqedvisiwdqslkpcvkltplcvtlnctnvtlgeikncsfditteirdktrkeyalf
yrldivplsntyrlincntstctqacpkvtfdpipihycapagyailkcnnktfngkgpc
nnvstvqcthgikpvvstqlllngslaeeeivirsknladnakiiivqlnksveivctrp
nnntrrsirigpgqtfyatdiigdirqaycnisgrnwseavnqvkkklkehfphknisfq
sssggdleitthsfncggeffycntsglfndtisnatimlpcrikqiinmwqevgkciya
ppikgnitcksditgllllrdgcntannaeifrpgggdmrdnwrselykykvvkieplgv
aptrckrrflgaagstmgaasmtltvqarnllsgivvwgikqlqarvlaverylrdqqll
giwgcsgklicctnvpwnsswsnrnlseiwdnmtwlqwdkeisnytqiiyglleesqnqq
ekneqdllal

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6myyF (F:)
mgwsciilflvatatgvhseivltqspatlslspgeratlscrasqsvssylawyqqkpg
qaprlliydasnratgiparfsgsgsgtdftltisslepedfavyycqqyeffgqgtkle
ikrtvaapsvfifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvte
qdskdstyslsstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >6myyF (F:)
eivltqspatlslspgeratlscrasqsvssylawyqqkpgqaprlliydasnratgipa
rfsgsgsgtdftltisslepedfavyycqqyeffgqgtkl

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6myyG (G:)
evqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwinpnsggtny
cqkfqgrvtmtrdtsistaymelsrlrsddtavyycargknsdynwdfqhwgqgtlvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthhhhhh

    Sequence, based on observed residues (ATOM records):
    >6myyG (G:)
evqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwinpnsggtny
cqkfqgrvtmtrdtsistaymelsrlrsddtavyycargknsdynwdfqhwgqgtlvtv

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6myyH (H:)
evqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwinpnsggtny
cqkfqgrvtmtrdtsistaymelsrlrsddtavyycargknsdynwdfqhwgqgtlvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkrvepkscdkthhhhhh

    Sequence, based on observed residues (ATOM records):
    >6myyH (H:)
evqlvqsgaevkkpgasvkvsckasgytftgyymhwvrqapgqglewmgwinpnsggtny
cqkfqgrvtmtrdtsistaymelsrlrsddtavyycargknsdynwdfqhwgqgtlvtv

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6myyL (L:)
mgwsciilflvatatgvhseivltqspatlslspgeratlscrasqsvssylawyqqkpg
qaprlliydasnratgiparfsgsgsgtdftltisslepedfavyycqqyeffgqgtkle
ikrtvaapsvfifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvte
qdskdstyslsstltlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records):
    >6myyL (L:)
eivltqspatlslspgeratlscrasqsvssylawyqqkpgqaprlliydasnratgipa
rfsgsgsgtdftltisslepedfavyycqqyeffgqgtkl