PDB entry 6w9g

View 6w9g on RCSB PDB site
Description: Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine in complex with CD40L at pH 6.8
Class: immune system
Keywords: Immunoglobulin, Cytokine, L-(7-hydroxycoumarin-4-yl)ethylglycine, IMMUNE SYSTEM
Deposited on 2020-03-23, released 2020-12-23
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-12-23, with a file datestamp of 2020-12-18.
Experiment type: XRAY
Resolution: 1.82 Å
R-factor: N/A
AEROSPACI score: 0.44 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: cd40 ligand
    Species: Homo sapiens [TaxId:9606]
    Gene: CD40LG, CD40L, TNFSF5, TRAP
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6w9ga_
  • Chain 'B':
    Compound: cd40 ligand
    Species: Homo sapiens [TaxId:9606]
    Gene: CD40LG, CD40L, TNFSF5, TRAP
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6w9gb_
  • Chain 'C':
    Compound: cd40 ligand
    Species: Homo sapiens [TaxId:9606]
    Gene: CD40LG, CD40L, TNFSF5, TRAP
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6w9gc_
  • Chain 'H':
    Compound: 5c8* Fab (heavy chain)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6W9G (0-End)
  • Chain 'K':
    Compound: 5c8* Fab (heavy chain)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6W9G (0-End)
  • Chain 'L':
    Compound: 5c8* Fab (light chain)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6W9G (0-End)
    Domains in SCOPe 2.08: d6w9gl1, d6w9gl2
  • Chain 'M':
    Compound: 5c8* Fab (light chain)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6W9G (0-End)
    Domains in SCOPe 2.08: d6w9gm1, d6w9gm2
  • Chain 'X':
    Compound: 5c8* Fab (heavy chain)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6W9G (0-End)
  • Chain 'Y':
    Compound: 5c8* Fab (light chain)
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6W9G (0-End)
    Domains in SCOPe 2.08: d6w9gy1, d6w9gy2
  • Heterogens: DV7, PEG, TRS, TMO, ETE, 1PE, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6w9gA (A:)
    gdqnpqiaahviseasskttsvlqwaekgyytmsnnlvtlengkqltvkrqglyyiyaqv
    tfcsnreassqapfiaslclkspgrferillraanthssakpcgqqsihlggvfelqpga
    svfvnvtdpsqvshgtgftsfgllkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >6w9gA (A:)
    npqiaahviseassktsvlqwaekgyytmsnnlvtlengkqltvkrqglyyiyaqvtfcs
    nrapfiaslclkspgrferillraanthssakpcgqqsihlggvfelqpgasvfvnvtdp
    sqvshgtgftsfgllkl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6w9gB (B:)
    gdqnpqiaahviseasskttsvlqwaekgyytmsnnlvtlengkqltvkrqglyyiyaqv
    tfcsnreassqapfiaslclkspgrferillraanthssakpcgqqsihlggvfelqpga
    svfvnvtdpsqvshgtgftsfgllkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >6w9gB (B:)
    npqiaahviseassktsvlqwaekgyytmsnnlvtlengkqltvkrqglyyiyaqvtfcs
    nrapfiaslclkspgrferillraanthssakpcgqqsihlggvfelqpgasvfvnvtdp
    sqvshgtgftsfgllkl
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6w9gC (C:)
    gdqnpqiaahviseasskttsvlqwaekgyytmsnnlvtlengkqltvkrqglyyiyaqv
    tfcsnreassqapfiaslclkspgrferillraanthssakpcgqqsihlggvfelqpga
    svfvnvtdpsqvshgtgftsfgllkl
    

    Sequence, based on observed residues (ATOM records): (download)
    >6w9gC (C:)
    npqiaahviseasskttsvlqwaekgyytmsnnlvtlengkqltvkrqglyyiyaqvtfc
    snrqapfiaslclkspgrferillraanthssakpcgqqsihlggvfelqpgasvfvnvt
    dpsqvshgtgftsfgllkl
    

  • Chain 'H':
    No sequence available.

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >6w9gL (L:)
    divltqspatlsvspgeratiscrasqrvssstysymhwyqqkpgqppkllikyasnles
    gvparfsgsgsgtdftltissvepedfatyycqhswexpptfgggtkleikrtvaapsvf
    ifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysls
    stltlskadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >6w9gL (L:)
    divltqspatlsvspgeratiscrasqrvssstysymhwyqqkpgqppkllikyasnles
    gvparfsgsgsgtdftltissvepedfatyycqhswexpptfgggtkleikrtvaapsvf
    ifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysls
    stltlskadyekhkvyacevthqglsspvtksfnr
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >6w9gM (M:)
    divltqspatlsvspgeratiscrasqrvssstysymhwyqqkpgqppkllikyasnles
    gvparfsgsgsgtdftltissvepedfatyycqhswexpptfgggtkleikrtvaapsvf
    ifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysls
    stltlskadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >6w9gM (M:)
    divltqspatlsvspgeratiscrasqrvssstysymhwyqqkpgqppkllikyasnles
    gvparfsgsgsgtdftltissvepedfatyycqhswexpptfgggtkleikrtvaapsvf
    ifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysls
    stltlskadyekhkvyacevthqglsspvtksfnrg
    

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    Sequence, based on SEQRES records: (download)
    >6w9gY (Y:)
    divltqspatlsvspgeratiscrasqrvssstysymhwyqqkpgqppkllikyasnles
    gvparfsgsgsgtdftltissvepedfatyycqhswexpptfgggtkleikrtvaapsvf
    ifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysls
    stltlskadyekhkvyacevthqglsspvtksfnrgec
    

    Sequence, based on observed residues (ATOM records): (download)
    >6w9gY (Y:)
    divltqspatlsvspgeratiscrasqrvssstysymhwyqqkpgqppkllikyasnles
    gvparfsgsgsgtdftltissvepedfatyycqhswexpptfgggtkleikrtvaapsvf
    ifppsdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstysls
    stltlskadyekhkvyacevthqglsspvtksfnrg