PDB entry 5yms

View 5yms on RCSB PDB site
Description: Structural basis of glycan specificity and identification of a novel glycan binding cavity in human P[19] rotavirus
Class: viral protein
Keywords: P[19] rotavirus, P[6] rotavirus, VP8*, Mucin core2core 2, Lacto-N-tetrarosetetraose (LNT), VIRAL PROTEIN
Deposited on 2017-10-22, released 2018-05-02
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-07-02.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: N/A
AEROSPACI score: 0.36 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9Q2P6 (1-160)
      • initiating methionine (0)
    Domains in SCOPe 2.08: d5ymsa_
  • Chain 'B':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9Q2P6 (1-160)
      • initiating methionine (0)
    Domains in SCOPe 2.08: d5ymsb_
  • Chain 'C':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymsc_
  • Chain 'D':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymsd_
  • Chain 'E':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymse_
  • Chain 'F':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymsf_
  • Chain 'G':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9Q2P6 (1-160)
      • initiating methionine (0)
    Domains in SCOPe 2.08: d5ymsg_
  • Chain 'H':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymsh_
  • Heterogens: A2G, GAL, NAG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymsA (A:)
mvldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslf
gvnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpn
attdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymsB (B:)
mvldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslf
gvnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpn
attdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5ymsC (C:)
mvldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslf
gvnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpn
attdysttsnlneisvttyaefyiiprsqeskcteyintgl

    Sequence, based on observed residues (ATOM records): (download) 
    >5ymsC (C:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5ymsD (D:)
mvldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslf
gvnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpn
attdysttsnlneisvttyaefyiiprsqeskcteyintgl

    Sequence, based on observed residues (ATOM records): (download) 
    >5ymsD (D:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >5ymsE (E:)
mvldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslf
gvnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpn
attdysttsnlneisvttyaefyiiprsqeskcteyintgl

    Sequence, based on observed residues (ATOM records): (download) 
    >5ymsE (E:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5ymsF (F:)
mvldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslf
gvnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpn
attdysttsnlneisvttyaefyiiprsqeskcteyintgl

    Sequence, based on observed residues (ATOM records): (download) 
    >5ymsF (F:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymsG (G:)
mvldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslf
gvnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpn
attdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >5ymsH (H:)
mvldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslf
gvnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpn
attdysttsnlneisvttyaefyiiprsqeskcteyintgl

    Sequence, based on observed residues (ATOM records): (download) 
    >5ymsH (H:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl