PDB entry 4laj

View 4laj on RCSB PDB site
Description: crystal structure of hiv-1 yu2 envelope gp120 glycoprotein in complex with cd4-mimetic miniprotein, m48u1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, jm4
Deposited on 2013-06-20, released 2013-08-14
The last revision was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: XRAY
Resolution: 2.14 Å
R-factor: N/A
AEROSPACI score: 0.36 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: HIV-1 YU2 gp120 envelope glycoprotein
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (Start-375)
  • Chain 'B':
    Compound: HIV-1 YU2 gp120 envelope glycoprotein
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (Start-375)
  • Chain 'C':
    Compound: cd4-mimetic miniprotein m48u1
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (0-End)
  • Chain 'D':
    Compound: cd4-mimetic miniprotein m48u1
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (0-End)
  • Chain 'F':
    Compound: HIV-1 YU2 gp120 envelope glycoprotein
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (Start-375)
  • Chain 'G':
    Compound: cd4-mimetic miniprotein m48u1
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (0-End)
  • Chain 'H':
    Compound: Llama single domain antibody, JM4
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (0-End)
  • Chain 'I':
    Compound: Llama single domain antibody, JM4
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (0-End)
  • Chain 'J':
    Compound: HIV-1 YU2 gp120 envelope glycoprotein
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (Start-375)
  • Chain 'K':
    Compound: cd4-mimetic miniprotein m48u1
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (0-End)
  • Chain 'L':
    Compound: Llama single domain antibody, JM4
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (0-End)
  • Chain 'M':
    Compound: Llama single domain antibody, JM4
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4LAJ (0-End)
  • Heterogens: NAG, EDO, ACA, HOH

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:
    >4lajA (A:)
mpmgslqplatlyllgmlvasvlavwkeatttlfcasdakaydtevhnvwathacvptdp
npqevklenvtenfnmwknnmveqmhediislwdqslkpcvkltggsvitqacpkvsfep
ipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngslaeeeivi
rsenftnnaktiivqlnesvvinctrpnnggsgsggdirqahcnlsktqwentleqiaik
lkeqfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitl
pcrikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmr
dnwrselykykvvkie

    Sequence, based on observed residues (ATOM records):
    >4lajA (A:)
vwkeatttlfcasdakaydtevhnvwathacvptdpnpqevklenvtenfnmwknnmveq
mhediislwdqslkpcvkltggsvitqacpkvsfepipihycapagfailkcndkkfngt
gpctnvstvqcthgirpvvstqlllngslaeeeivirsenftnnaktiivqlnesvvinc
trpnngdirqahcnlsktqwentleqiaiklkeqfgnnktiifnpssggdpeivthsfnc
ggeffycnstqlftwndtrklnntgrnitlpcrikqiinmwqevgkamyappirgqircs
snitgllltrdggngteifrpgggdmrdnwrselykykvvkie

  • Chain 'B':
    Sequence, based on SEQRES records:
    >4lajB (B:)
mpmgslqplatlyllgmlvasvlavwkeatttlfcasdakaydtevhnvwathacvptdp
npqevklenvtenfnmwknnmveqmhediislwdqslkpcvkltggsvitqacpkvsfep
ipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngslaeeeivi
rsenftnnaktiivqlnesvvinctrpnnggsgsggdirqahcnlsktqwentleqiaik
lkeqfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitl
pcrikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmr
dnwrselykykvvkie

    Sequence, based on observed residues (ATOM records):
    >4lajB (B:)
vwkeatttlfcasdakaydtevhnvwathacvptdpnpqevklenvtenfnmwknnmveq
mhediislwdqslkpcvkltggsvitqacpkvsfepipihycapagfailkcndkkfngt
gpctnvstvqcthgirpvvstqlllngslaeeeivirsenftnnaktiivqlnesvvinc
trpnngdirqahcnlsktqwentleqiaiklkeqfgnnktiifnpssggdpeivthsfnc
ggeffycnstqlftwndtrkltgrnitlpcrikqiinmwqevgkamyappirgqircssn
itgllltrdggngteifrpgggdmrdnwrselykykvvkie

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >4lajC (C:)
xnlhfcqlrckslgllgrcaptxcacv

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >4lajD (D:)
xnlhfcqlrckslgllgrcaptxcacv

  • Chain 'F':
    Sequence, based on SEQRES records:
    >4lajF (F:)
mpmgslqplatlyllgmlvasvlavwkeatttlfcasdakaydtevhnvwathacvptdp
npqevklenvtenfnmwknnmveqmhediislwdqslkpcvkltggsvitqacpkvsfep
ipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngslaeeeivi
rsenftnnaktiivqlnesvvinctrpnnggsgsggdirqahcnlsktqwentleqiaik
lkeqfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitl
pcrikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmr
dnwrselykykvvkie

    Sequence, based on observed residues (ATOM records):
    >4lajF (F:)
vwkeatttlfcasdakaydtevhnvwathacvptdpnpqevklenvtenfnmwknnmveq
mhediislwdqslkpcvkltggsvitqacpkvsfepipihycapagfailkcndkkfngt
gpctnvstvqcthgirpvvstqlllngslaeeeivirsenftnnaktiivqlnesvvinc
trpnngdirqahcnlsktqwentleqiaiklkeqfgnnktiifnpssggdpeivthsfnc
ggeffycnstqlftwgrnitlpcrikqiinmwqevgkamyappirgqircssnitglllt
rdggngteifrpgggdmrdnwrselykykvvkie

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records:
    >4lajG (G:)
xnlhfcqlrckslgllgrcaptxcacv

  • Chain 'H':
    Sequence, based on SEQRES records:
    >4lajH (H:)
evqlvesggglvqpggslrlscaasgftldyysigwfrqapgkeregvscisdsdgrtyy
adsvkgrftisrdnakntvylqmnslkpedtavyycatdctvdpsllyvmdyygkgtqvt
vssaaaeqk

    Sequence, based on observed residues (ATOM records):
    >4lajH (H:)
evqlvesggglvqpggslrlscaasgftldyysigwfrqapgkeregvscisdsdgrtyy
adsvkgrftisrdnakntvylqmnslkpedtavyycatdctvdpsllyvmdyygkgtqvt
vssa

  • Chain 'I':
    Sequence, based on SEQRES records:
    >4lajI (I:)
evqlvesggglvqpggslrlscaasgftldyysigwfrqapgkeregvscisdsdgrtyy
adsvkgrftisrdnakntvylqmnslkpedtavyycatdctvdpsllyvmdyygkgtqvt
vssaaaeqk

    Sequence, based on observed residues (ATOM records):
    >4lajI (I:)
evqlvesggglvqpggslrlscaasgftldyysigwfrqapgkeregvscisdsdgrtyy
adsvkgrftisrdnakntvylqmnslkpedtavyycatdctvdpsllyvmdyygkgtqvt
vssaa

  • Chain 'J':
    Sequence, based on SEQRES records:
    >4lajJ (J:)
mpmgslqplatlyllgmlvasvlavwkeatttlfcasdakaydtevhnvwathacvptdp
npqevklenvtenfnmwknnmveqmhediislwdqslkpcvkltggsvitqacpkvsfep
ipihycapagfailkcndkkfngtgpctnvstvqcthgirpvvstqlllngslaeeeivi
rsenftnnaktiivqlnesvvinctrpnnggsgsggdirqahcnlsktqwentleqiaik
lkeqfgnnktiifnpssggdpeivthsfncggeffycnstqlftwndtrklnntgrnitl
pcrikqiinmwqevgkamyappirgqircssnitgllltrdggkdtngteifrpgggdmr
dnwrselykykvvkie

    Sequence, based on observed residues (ATOM records):
    >4lajJ (J:)
vwkeatttlfcasdakaydtevhnvwathacvptdpnpqevklenvtenfnmwknnmveq
mhediislwdqslkpcvkltggsvitqacpkvsfepipihycapagfailkcndkkfngt
gpctnvstvqcthgirpvvstqlllngslaeeeivirsenftnnaktiivqlnesvvinc
trpnngdirqahcnlsktqwentleqiaiklkeqfgnnktiifnpssggdpeivthsfnc
ggeffycnstqlftwndtgrnitlpcrikqiinmwqevgkamyappirgqircssnitgl
lltrdggngteifrpgggdmrdnwrselykykvvkie

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records:
    >4lajK (K:)
xnlhfcqlrckslgllgrcaptxcacv

  • Chain 'L':
    Sequence, based on SEQRES records:
    >4lajL (L:)
evqlvesggglvqpggslrlscaasgftldyysigwfrqapgkeregvscisdsdgrtyy
adsvkgrftisrdnakntvylqmnslkpedtavyycatdctvdpsllyvmdyygkgtqvt
vssaaaeqk

    Sequence, based on observed residues (ATOM records):
    >4lajL (L:)
evqlvesggglvqpggslrlscaasgftldyysigwfrqapgkeregvscisdsdgrtyy
adsvkgrftisrdnakntvylqmnslkpedtavyycatdctvdpsllyvmdyygkgtqvt
vss

  • Chain 'M':
    Sequence, based on SEQRES records:
    >4lajM (M:)
evqlvesggglvqpggslrlscaasgftldyysigwfrqapgkeregvscisdsdgrtyy
adsvkgrftisrdnakntvylqmnslkpedtavyycatdctvdpsllyvmdyygkgtqvt
vssaaaeqk

    Sequence, based on observed residues (ATOM records):
    >4lajM (M:)
evqlvesggglvqpggslrlscaasgftldyysigwfrqapgkeregvscisdsdgrtyy
adsvkgrftisrdnakntvylqmnslkpedtavyycatdctvdpsllyvmdyygkgtqvt
vss