PDB entry 6xw7

View 6xw7 on RCSB PDB site
Description: Crystal structure of murine norovirus P domain in complex with Nanobody NB-5829 and glycochenodeoxycholate (GCDCA)
Class: viral protein
Keywords: MNV, neutralizing nanobody, VHH, norovirus, VIRAL PROTEIN
Deposited on 2020-01-23, released 2020-04-22
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-01, with a file datestamp of 2020-06-26.
Experiment type: XRAY
Resolution: 2.15 Å
R-factor: N/A
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: capsid protein
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q80J94 (1-End)
      • expression tag (0)
    Domains in SCOPe 2.08: d6xw7a1, d6xw7a2
  • Chain 'B':
    Compound: capsid protein
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6xw7b_
  • Chain 'C':
    Compound: Nanobody NB-5829
    Species: Vicugna pacos [TaxId:30538]
    Database cross-references and differences (RAF-indexed):
    • PDB 6XW7 (0-End)
    Domains in SCOPe 2.08: d6xw7c1, d6xw7c2, d6xw7c3
  • Chain 'D':
    Compound: Nanobody NB-5829
    Species: Vicugna pacos [TaxId:30538]
    Database cross-references and differences (RAF-indexed):
    • PDB 6XW7 (0-End)
    Domains in SCOPe 2.08: d6xw7d1, d6xw7d2, d6xw7d3
  • Chain 'E':
    Compound: capsid protein
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6xw7e_
  • Chain 'F':
    Compound: capsid protein
    Species: Murine norovirus 1 [TaxId:223997]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6xw7f_
  • Chain 'G':
    Compound: Nanobody NB-5829
    Species: Vicugna pacos [TaxId:30538]
    Database cross-references and differences (RAF-indexed):
    • PDB 6XW7 (0-End)
    Domains in SCOPe 2.08: d6xw7g1, d6xw7g2, d6xw7g3
  • Chain 'H':
    Compound: Nanobody NB-5829
    Species: Vicugna pacos [TaxId:30538]
    Database cross-references and differences (RAF-indexed):
    • PDB 6XW7
    Domains in SCOPe 2.08: d6xw7h1, d6xw7h2
  • Heterogens: CHO, EDO, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6xw7A (A:)
siyrmvdlpviqprlctharwpapvygllvdpslpsnpqwqngrvhvdgtllgttpisgs
wvscfaaeaaykfqsgtgevatftlieqdgsayvpgdraaplgypdfsgqleievqtett
ktgdklkvttfemilgpttnadqapyqgrvfasvtaaasldlvdgrvravprsiygfqdt
ipeyndgllvplappigpflpgevllrfrtymrqidtadaaaeaidcalpqefvswfasn
aftvqsealllryrntltgqllfecklynegyialsysgsgpltfptdgifevvswvprl
yqlasvgsl

    Sequence, based on observed residues (ATOM records): (download) 
    >6xw7A (A:)
siyrmvdlpviqprlctharwpapvygllvdpslpsnpqwqngrvhvdgtllgttpisgs
wvscfaaeaaykfqsgtgevatftlieqdgsayvpgdraaplgypdfsgqleievqtett
ktgdklkvttfemilgptdqapyqgrvfasvtaaasldlvdgrvravprsiygfqdtipe
yndgllvplappigpflpgevllrfrtymrqidtadaaaeaidcalpqefvswfasnaft
vqsealllryrntltgqllfecklynegyialsysgsgpltfptdgifevvswvprlyql
asv

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6xw7B (B:)
siyrmvdlpviqprlctharwpapvygllvdpslpsnpqwqngrvhvdgtllgttpisgs
wvscfaaeaaykfqsgtgevatftlieqdgsayvpgdraaplgypdfsgqleievqtett
ktgdklkvttfemilgpttnadqapyqgrvfasvtaaasldlvdgrvravprsiygfqdt
ipeyndgllvplappigpflpgevllrfrtymrqidtadaaaeaidcalpqefvswfasn
aftvqsealllryrntltgqllfecklynegyialsysgsgpltfptdgifevvswvprl
yqlasvgsl

    Sequence, based on observed residues (ATOM records): (download) 
    >6xw7B (B:)
rmvdlpviqprlctharwpapvygllvdpslpsnpqwqngrvhvdgtllgttpisgswvs
cfaaeaaykfqsgtgevatftlieqdgsayvpgdraaplgypdfsgqleievqtettktg
dklkvttfemilgpttnadqapyqgrvfasvtaaasldlvdgrvravprsiygfqdtipe
yndgllvplappigpflpgevllrfrtymrqidtadaaaeaidcalpqefvswfasnaft
vqsealllryrntltgqllfecklynegyialsysgsgpltfptdgifevvswvprlyql
asvgs

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6xw7C (C:)
qvqlqesggglveaggslrlsclgsgltfsryamgwfrqapgkerefvasitrsggspny
adsvkgrftisrdnakntvylqmsslkpedtavyycagrgsvyydvwgqgtqvtvsshhh
hhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6xw7C (C:)
qvqlqesggglveaggslrlsclgsgltfsryamgwfrqapgkerefvasitrsggspny
adsvkgrftisrdnakntvylqmsslkpedtavyycagrgsvyydvwgqgtqvtvss

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6xw7D (D:)
qvqlqesggglveaggslrlsclgsgltfsryamgwfrqapgkerefvasitrsggspny
adsvkgrftisrdnakntvylqmsslkpedtavyycagrgsvyydvwgqgtqvtvsshhh
hhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6xw7D (D:)
qvqlqesggglveaggslrlsclgsgltfsryamgwfrqapgkerefvasitrsggspny
adsvkgrftisrdnakntvylqmsslkpedtavyycagrgsvyydvwgqgtqvtvss

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >6xw7E (E:)
siyrmvdlpviqprlctharwpapvygllvdpslpsnpqwqngrvhvdgtllgttpisgs
wvscfaaeaaykfqsgtgevatftlieqdgsayvpgdraaplgypdfsgqleievqtett
ktgdklkvttfemilgpttnadqapyqgrvfasvtaaasldlvdgrvravprsiygfqdt
ipeyndgllvplappigpflpgevllrfrtymrqidtadaaaeaidcalpqefvswfasn
aftvqsealllryrntltgqllfecklynegyialsysgsgpltfptdgifevvswvprl
yqlasvgsl

    Sequence, based on observed residues (ATOM records): (download) 
    >6xw7E (E:)
rmvdlpviqprlctharwpapvygllvdpslpsnpqwqngrvhvdgtllgttpisgswvs
cfaaeaaykfqsgtgevatftlieqdgsayvpgdraaplgypdfsgqleievqtettktg
dklkvttfemilgpttnadqapyqgrvfasvtaaasldlvdgrvravprsiygfqdtipe
yndgllvplappigpflpgevllrfrtymrqidtadaaaeaidcalpqefvswfasnaft
vqsealllryrntltgqllfecklynegyialsysgsgpltfptdgifevvswvprlyql
asv

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6xw7F (F:)
siyrmvdlpviqprlctharwpapvygllvdpslpsnpqwqngrvhvdgtllgttpisgs
wvscfaaeaaykfqsgtgevatftlieqdgsayvpgdraaplgypdfsgqleievqtett
ktgdklkvttfemilgpttnadqapyqgrvfasvtaaasldlvdgrvravprsiygfqdt
ipeyndgllvplappigpflpgevllrfrtymrqidtadaaaeaidcalpqefvswfasn
aftvqsealllryrntltgqllfecklynegyialsysgsgpltfptdgifevvswvprl
yqlasvgsl

    Sequence, based on observed residues (ATOM records): (download) 
    >6xw7F (F:)
rmvdlpviqprlctharwpapvygllvdpslpsnpqwqngrvhvdgtllgttpisgswvs
cfaaeaaykfqsgtgevatftlieqdgsayvpgdraaplgypdfsgqleievqtettktg
dklkvttfemilgpdqapyqgrvfasvtaaasldlvdgrvravprsiygfqdtipeyndg
llvplappigpflpgevllrfrtymrqidtadaaaeaidcalpqefvswfasnaftvqse
alllryrntltgqllfecklynegyialsysgsgpltfptdgifevvswvprlyqlasvg
s

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >6xw7G (G:)
qvqlqesggglveaggslrlsclgsgltfsryamgwfrqapgkerefvasitrsggspny
adsvkgrftisrdnakntvylqmsslkpedtavyycagrgsvyydvwgqgtqvtvsshhh
hhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6xw7G (G:)
qvqlqesggglveaggslrlsclgsgltfsryamgwfrqapgkerefvasitrsggspny
adsvkgrftisrdnakntvylqmsslkpedtavyycagrgsvyydvwgqgtqvtvss

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >6xw7H (H:)
qvqlqesggglveaggslrlsclgsgltfsryamgwfrqapgkerefvasitrsggspny
adsvkgrftisrdnakntvylqmsslkpedtavyycagrgsvyydvwgqgtqvtvsshhh
hhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6xw7H (H:)
vqlqesggglveaggslrlsclgsgltfsryamgwfrqapgkerefvasitrsggspnya
dsvkgrftisrdnakntvylqmsslkpedtavyycagrgsvyydvwgqgtqvtv