PDB entry 6o41

View 6o41 on RCSB PDB site
Description: Crystal structure of the unbound PGZL1 germline Fab fragment (PGZL1_gVmDmJ)
Class: immune system
Keywords: germline PGZL1 ANTI HIV-1, GP41 MPER, MEMBRANE LIPIDS, BROADLY NEUTRALISING HIV-1 ANTIBODY, IMMUNE SYSTEM
Deposited on 2019-02-27, released 2019-12-04
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-12-11, with a file datestamp of 2019-12-06.
Experiment type: XRAY
Resolution: 2.47 Å
R-factor: N/A
AEROSPACI score: 0.21 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: germline PGZL1_gVmDmJ light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6O41
    Domains in SCOPe 2.08: d6o41a1, d6o41a2
  • Chain 'B':
    Compound: germline PGZL1_gVmDmJ heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6O41 (0-End)
  • Chain 'C':
    Compound: germline PGZL1_gVmDmJ light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6O41
    Domains in SCOPe 2.08: d6o41c1, d6o41c2
  • Chain 'D':
    Compound: germline PGZL1_gVmDmJ heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6O41 (0-End)
  • Chain 'H':
    Compound: germline PGZL1_gVmDmJ heavy chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6O41 (0-End)
  • Chain 'L':
    Compound: germline PGZL1_gVmDmJ light chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6O41
    Domains in SCOPe 2.08: d6o41l1, d6o41l2
  • Chain 'M':
    Compound: Immunoglobulin G-binding protein G (DOMAIN III)
    Species: Streptococcus sp. group G [TaxId:1320]
    Gene: spg
    Database cross-references and differences (RAF-indexed):
    • Uniprot P19909 (Start-60)
      • expression tag (61-63)
    Domains in SCOPe 2.08: d6o41m1, d6o41m2
  • Chain 'N':
    Compound: Immunoglobulin G-binding protein G (DOMAIN III)
    Species: Streptococcus sp. group G [TaxId:1320]
    Gene: spg
    Database cross-references and differences (RAF-indexed):
    • Uniprot P19909 (Start-60)
      • expression tag (61-63)
    Domains in SCOPe 2.08: d6o41n1, d6o41n2
  • Chain 'O':
    Compound: Immunoglobulin G-binding protein G (DOMAIN III)
    Species: Streptococcus sp. group G [TaxId:1320]
    Gene: spg
    Database cross-references and differences (RAF-indexed):
    • Uniprot P19909 (Start-60)
      • expression tag (61-62)
    Domains in SCOPe 2.08: d6o41o1, d6o41o2
  • Heterogens: GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6o41A (A:)
eivltqspgtlslspgeratlscrasqsvsssylawyqqkpgqaprlliygassratgip
drfsgsgsgtdftltisrlepedfavyycqqygtsqstfgqgtrleikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >6o41A (A:)
ivltqspgtlslspgeratlscrasqsvsssylawyqqkpgqaprlliygassratgipd
rfsgsgsgtdftltisrlepedfavyycqqygtsqstfgqgtrleikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6o41C (C:)
eivltqspgtlslspgeratlscrasqsvsssylawyqqkpgqaprlliygassratgip
drfsgsgsgtdftltisrlepedfavyycqqygtsqstfgqgtrleikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >6o41C (C:)
ivltqspgtlslspgeratlscrasqsvsssylawyqqkpgqaprlliygassratgipd
rfsgsgsgtdftltisrlepedfavyycqqygtsqstfgqgtrleikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'D':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >6o41L (L:)
eivltqspgtlslspgeratlscrasqsvsssylawyqqkpgqaprlliygassratgip
drfsgsgsgtdftltisrlepedfavyycqqygtsqstfgqgtrleikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >6o41L (L:)
ivltqspgtlslspgeratlscrasqsvsssylawyqqkpgqaprlliygassratgipd
rfsgsgsgtdftltisrlepedfavyycqqygtsqstfgqgtrleikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >6o41M (M:)
mtpavttyklvingktlkgetttkavdaetaekafkqyandngvdgvwtyddatktftvt
ehhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6o41M (M:)
vttyklvingktlkgetttkavdaetaekafkqyandngvdgvwtyddatktftvtehhh

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >6o41N (N:)
mtpavttyklvingktlkgetttkavdaetaekafkqyandngvdgvwtyddatktftvt
ehhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6o41N (N:)
vttyklvingktlkgetttkavdaetaekafkqyandngvdgvwtyddatktftvtehhh

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >6o41O (O:)
mtpavttyklvingktlkgetttkavdaetaekafkqyandngvdgvwtyddatktftvt
ehhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6o41O (O:)
vttyklvingktlkgetttkavdaetaekafkqyandngvdgvwtyddatktftvtehh