PDB entry 4d9l

View 4d9l on RCSB PDB site
Description: Fab structure of anti-HIV-1 gp120 V2 mAb 697
Class: immune system
Keywords: Ig, antibody, HIV-1 gp120, IMMUNE SYSTEM
Deposited on 2012-01-11, released 2012-03-21
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-08-02, with a file datestamp of 2017-07-28.
Experiment type: XRAY
Resolution: 2.49 Å
R-factor: N/A
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'H':
    Compound: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9L (0-115)
    • Uniprot Q6GMX6 (116-End)
    Domains in SCOPe 2.08: d4d9lh_
  • Chain 'I':
    Compound: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9L (0-115)
    • Uniprot Q6GMX6 (116-End)
    Domains in SCOPe 2.08: d4d9li_
  • Chain 'J':
    Compound: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9L (0-115)
    • Uniprot Q6GMX6 (116-222)
    Domains in SCOPe 2.08: d4d9lj_
  • Chain 'K':
    Compound: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9L (0-115)
    • Uniprot Q6GMX6 (116-End)
    Domains in SCOPe 2.08: d4d9lk_
  • Chain 'L':
    Compound: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9l (0-119)
    • Uniprot Q6GMX4 (120-End)
    Domains in SCOPe 2.08: d4d9ll1, d4d9ll2
  • Chain 'M':
    Compound: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9l (0-119)
    • Uniprot Q6GMX4 (120-214)
    Domains in SCOPe 2.08: d4d9lm1, d4d9lm2
  • Chain 'N':
    Compound: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9l (0-119)
    • Uniprot Q6GMX4 (120-214)
    Domains in SCOPe 2.08: d4d9ln1, d4d9ln2
  • Chain 'O':
    Compound: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 697
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9l (0-119)
    • Uniprot Q6GMX4 (120-214)
    Domains in SCOPe 2.08: d4d9lo1, d4d9lo2
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >4d9lH (H:)
qvqlvqsgaevkkpgssvkvsckasggnfntytiswvrqapgqglewmgriipifgivnp
aqkfpgrvtinvdkstntaymelsslrsedtavyycatsgvglhfgyfdywgqgtqvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepks

    Sequence, based on observed residues (ATOM records): (download) 
    >4d9lH (H:)
qvqlvqsgaevkkpgssvkvsckasggnfntytiswvrqapgqglewmgriipifgivnp
aqkfpgrvtinvdkstntaymelsslrsedtavyycatsgvglhfgyfdywgqgtqvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >4d9lI (I:)
qvqlvqsgaevkkpgssvkvsckasggnfntytiswvrqapgqglewmgriipifgivnp
aqkfpgrvtinvdkstntaymelsslrsedtavyycatsgvglhfgyfdywgqgtqvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepks

    Sequence, based on observed residues (ATOM records): (download) 
    >4d9lI (I:)
qvqlvqsgaevkkpgssvkvsckasggnfntytiswvrqapgqglewmgriipifgivnp
aqkfpgrvtinvdkstntaymelsslrsedtavyycatsgvglhfgyfdywgqgtqvtvs
sastkgpsvfplapssggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssgly
slssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4d9lJ (J:)
qvqlvqsgaevkkpgssvkvsckasggnfntytiswvrqapgqglewmgriipifgivnp
aqkfpgrvtinvdkstntaymelsslrsedtavyycatsgvglhfgyfdywgqgtqvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepks

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >4d9lK (K:)
qvqlvqsgaevkkpgssvkvsckasggnfntytiswvrqapgqglewmgriipifgivnp
aqkfpgrvtinvdkstntaymelsslrsedtavyycatsgvglhfgyfdywgqgtqvtvs
sastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqs
sglyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepks

    Sequence, based on observed residues (ATOM records): (download) 
    >4d9lK (K:)
qvqlvqsgaevkkpgssvkvsckasggnfntytiswvrqapgqglewmgriipifgivnp
aqkfpgrvtinvdkstntaymelsslrsedtavyycatsgvglhfgyfdywgqgtqvtvs
sastkgpsvfplapsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglys
lssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >4d9lL (L:)
qsvltqppsvsgapgqrvtisctgsssnigahydvhwyqqlpgtapklliygnsnrpsgv
pdrfsgsksgtsaslaitglqaedeadyycqsydsslsgyvfgtgtkvtvlgqpkanptv
tlfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaas
sylsltpeqwkshrsyscqvthegstvektvapte

    Sequence, based on observed residues (ATOM records): (download) 
    >4d9lL (L:)
qsvltqppsvsgapgqrvtisctgsssnigahydvhwyqqlpgtapklliygnsnrpsgv
pdrfsgsksgtsaslaitglqaedeadyycqsydsslsgyvfgtgtkvtvlgqpkanptv
tlfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaas
sylsltpeqwkshrsyscqvthegstvektvapt

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4d9lM (M:)
qsvltqppsvsgapgqrvtisctgsssnigahydvhwyqqlpgtapklliygnsnrpsgv
pdrfsgsksgtsaslaitglqaedeadyycqsydsslsgyvfgtgtkvtvlgqpkanptv
tlfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaas
sylsltpeqwkshrsyscqvthegstvektvapte

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4d9lN (N:)
qsvltqppsvsgapgqrvtisctgsssnigahydvhwyqqlpgtapklliygnsnrpsgv
pdrfsgsksgtsaslaitglqaedeadyycqsydsslsgyvfgtgtkvtvlgqpkanptv
tlfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaas
sylsltpeqwkshrsyscqvthegstvektvapte

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4d9lO (O:)
qsvltqppsvsgapgqrvtisctgsssnigahydvhwyqqlpgtapklliygnsnrpsgv
pdrfsgsksgtsaslaitglqaedeadyycqsydsslsgyvfgtgtkvtvlgqpkanptv
tlfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpskqsnnkyaas
sylsltpeqwkshrsyscqvthegstvektvapte