PDB entry 1ybd

View 1ybd on RCSB PDB site
Description: Crystal structure analysis of uridylate kinase from Neisseria meningitidis
Class: transferase
Keywords: alpha/beta/alpha fold, Kinase, Hexamer, Structural Genomics, Protein Structure Initiative, PSI, New York SGX Research Center for Structural Genomics, NYSGXRC, T1843, TRANSFERASE
Deposited on 2004-12-20, released 2005-02-15
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: 0.206
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: uridylate kinase
    Species: Neisseria meningitidis [TaxId:487]
    Gene: pyrH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P65932 (Start-238)
      • modified residue (19)
      • modified residue (44)
      • modified residue (68)
      • modified residue (76)
      • modified residue (78-79)
      • modified residue (83)
      • modified residue (107)
      • modified residue (153)
      • modified residue (158)
      • modified residue (197)
    Domains in SCOPe 2.07: d1ybda1
  • Chain 'B':
    Compound: uridylate kinase
    Species: Neisseria meningitidis [TaxId:487]
    Gene: pyrH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P65932 (Start-238)
      • modified residue (19)
      • modified residue (44)
      • modified residue (68)
      • modified residue (76)
      • modified residue (78-79)
      • modified residue (83)
      • modified residue (107)
      • modified residue (153)
      • modified residue (158)
      • modified residue (197)
    Domains in SCOPe 2.07: d1ybdb_
  • Chain 'C':
    Compound: uridylate kinase
    Species: Neisseria meningitidis [TaxId:487]
    Gene: pyrH
    Database cross-references and differences (RAF-indexed):
    • Uniprot P65932 (Start-238)
      • modified residue (19)
      • modified residue (44)
      • modified residue (68)
      • modified residue (76)
      • modified residue (78-79)
      • modified residue (83)
      • modified residue (107)
      • modified residue (153)
      • modified residue (158)
      • modified residue (197)
    Domains in SCOPe 2.07: d1ybdc_
  • Heterogens: FMT, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >1ybdA (A:)
mtqqikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifr
gvsaqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpka
iqyleegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsat
ryetitfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc

    Sequence, based on observed residues (ATOM records): (download) 
    >1ybdA (A:)
qikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifrgvs
aqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpkaiqy
leegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsatrye
titfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >1ybdB (B:)
mtqqikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifr
gvsaqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpka
iqyleegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsat
ryetitfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc

    Sequence, based on observed residues (ATOM records): (download) 
    >1ybdB (B:)
qikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifrgvs
aqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpkaiqy
leegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsatrye
titfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >1ybdC (C:)
mtqqikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifr
gvsaqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpka
iqyleegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsat
ryetitfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc

    Sequence, based on observed residues (ATOM records): (download) 
    >1ybdC (C:)
qikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifrgvs
aqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpkaiqy
leegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsatrye
titfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc