PDB entry 4krm

View 4krm on RCSB PDB site
Description: Nanobody/VHH domain 7D12 in complex with domain III of the extracellular region of EGFR, pH 3.5
Class: transferase/immune system
Keywords: cell surface receptor, glycoprotein, nanobody, VHH domain, Camelid VH domain, antibody, antigen, antibody complex, TRANSFERASE-IMMUNE SYSTEM complex
Deposited on 2013-05-16, released 2013-08-28
The last revision prior to the SCOPe 2.07 freeze date was dated 2013-08-28, with a file datestamp of 2013-08-23.
Experiment type: XRAY
Resolution: 2.65 Å
R-factor: 0.21
AEROSPACI score: 0.31 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Epidermal growth factor receptor
    Species: Homo sapiens [TaxId:9606]
    Gene: EGFR, ERBB, ERBB1, HER1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00533 (4-End)
      • expression tag (0-3)
    Domains in SCOPe 2.07: d4krma1, d4krma2, d4krma3
  • Chain 'B':
    Compound: Nanobody/VHH domain 7D12
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KRM (0-End)
    Domains in SCOPe 2.07: d4krmb_
  • Chain 'C':
    Compound: Epidermal growth factor receptor
    Species: Homo sapiens [TaxId:9606]
    Gene: EGFR, ERBB, ERBB1, HER1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00533 (4-End)
      • expression tag (0-3)
    Domains in SCOPe 2.07: d4krmc1, d4krmc2, d4krmc3
  • Chain 'D':
    Compound: Nanobody/VHH domain 7D12
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KRM (0-End)
    Domains in SCOPe 2.07: d4krmd_
  • Chain 'E':
    Compound: Epidermal growth factor receptor
    Species: Homo sapiens [TaxId:9606]
    Gene: EGFR, ERBB, ERBB1, HER1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00533 (4-End)
      • expression tag (0-3)
    Domains in SCOPe 2.07: d4krme1, d4krme2, d4krme3
  • Chain 'F':
    Compound: Nanobody/VHH domain 7D12
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KRM (0-End)
    Domains in SCOPe 2.07: d4krmf_
  • Chain 'G':
    Compound: Epidermal growth factor receptor
    Species: Homo sapiens [TaxId:9606]
    Gene: EGFR, ERBB, ERBB1, HER1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00533 (4-End)
      • expression tag (0-3)
    Domains in SCOPe 2.07: d4krmg1, d4krmg2
  • Chain 'H':
    Compound: Nanobody/VHH domain 7D12
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KRM (0-End)
    Domains in SCOPe 2.07: d4krmh_
  • Chain 'I':
    Compound: Epidermal growth factor receptor
    Species: Homo sapiens [TaxId:9606]
    Gene: EGFR, ERBB, ERBB1, HER1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00533 (4-End)
      • expression tag (0-3)
    Domains in SCOPe 2.07: d4krmi1, d4krmi2, d4krmi3
  • Chain 'J':
    Compound: Nanobody/VHH domain 7D12
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KRM (0-End)
    Domains in SCOPe 2.07: d4krmj_
  • Chain 'K':
    Compound: Epidermal growth factor receptor
    Species: Homo sapiens [TaxId:9606]
    Gene: EGFR, ERBB, ERBB1, HER1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P00533 (4-End)
      • expression tag (0-3)
    Domains in SCOPe 2.07: d4krmk1, d4krmk2, d4krmk3
  • Chain 'L':
    Compound: Nanobody/VHH domain 7D12
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KRM (0-End)
    Domains in SCOPe 2.07: d4krml_
  • Heterogens: NAG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4krmA (A:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscrnvsrgrecvdkhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmA (A:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscr
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4krmB (B:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvssalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmB (B:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvss
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4krmC (C:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscrnvsrgrecvdkhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmC (C:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscr
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4krmD (D:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvssalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmD (D:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvss
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4krmE (E:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscrnvsrgrecvdkhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmE (E:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscr
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4krmF (F:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvssalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmF (F:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tv
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >4krmG (G:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscrnvsrgrecvdkhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmG (G:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscrc
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >4krmH (H:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvssalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmH (H:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvss
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >4krmI (I:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscrnvsrgrecvdkhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmI (I:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvs
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >4krmJ (J:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvssalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmJ (J:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvss
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >4krmK (K:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvscrnvsrgrecvdkhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmK (K:)
    leekkvcngigigefkdslsinatnikhfknctsisgdlhilpvafrgdsfthtppldpq
    eldilktvkeitgflliqawpenrtdlhafenleiirgrtkqhgqfslavvslnitslgl
    rslkeisdgdviisgnknlcyantinwkklfgtsgqktkiisnrgensckatgqvchalc
    spegcwgpeprdcvsc
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >4krmL (L:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvssalehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4krmL (L:)
    qvkleesgggsvqtggslrltcaasgrtsrsygmgwfrqapgkerefvsgiswrgdstgy
    adsvkgrftisrdnakntvdlqmnslkpedtaiyycaaaagsawygtlyeydywgqgtqv
    tvss