PDB entry 5ymt

View 5ymt on RCSB PDB site
Description: Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens
Class: viral protein
Keywords: Rotavirus, P[19] VP8*, 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: 2.2 Å
R-factor: N/A
AEROSPACI score: 0.34 (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): Domains in SCOPe 2.08: d5ymta_
  • Chain 'B':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymtb_
  • 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: d5ymtc_
  • 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: d5ymtd_
  • 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: d5ymte_
  • 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: d5ymtf_
  • Chain 'G':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymtg_
  • 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: d5ymth_
  • Chain 'I':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymti_
  • Chain 'J':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymtj_
  • Chain 'K':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymtk_
  • Chain 'L':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymtl_
  • Chain 'M':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymtm_
  • Chain 'N':
    Compound: Outer capsid protein VP4
    Species: Human rotavirus A [TaxId:10941]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5ymtn_
  • Heterogens: GAL, GLC, NAG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtA (A:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtB (B:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtC (C:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtD (D:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtE (E:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtF (F:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtG (G:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtH (H:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtI (I:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtJ (J:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtK (K:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtL (L:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtM (M:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5ymtN (N:)
vldgpyqpvafkppndywilvnsnsngvvlegtnntdvwvaiisiepnvnsesrqyslfg
vnkqitvvntsnkwkfmemfrnnsnaefqhkrtltsstklvgilkhggrlwtyhgetpna
ttdysttsnlneisvttyaefyiiprsqeskcteyintgl