PDB entry 2va1

View 2va1 on RCSB PDB site
Description: crystal structure of ump kinase from ureaplasma parvum
Class: transferase
Keywords: umpk, kinase, transferase, uridylate kinase, pyrimidine biosynthesis, amino acid kinase family
Deposited on 2007-08-28, released 2007-09-18
The last revision prior to the SCOPe 2.08 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.235
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: uridylate kinase
    Species: Ureaplasma parvum [TaxId:134821]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VA1
    • Uniprot Q9PPX6 (Start-255)
    Domains in SCOPe 2.08: d2va1a_
  • Chain 'B':
    Compound: uridylate kinase
    Species: Ureaplasma parvum [TaxId:134821]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VA1 (Start-20)
    • Uniprot Q9PPX6 (21-255)
    Domains in SCOPe 2.08: d2va1b1, d2va1b2
  • Chain 'C':
    Compound: uridylate kinase
    Species: Ureaplasma parvum [TaxId:134821]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VA1
    • Uniprot Q9PPX6 (Start-255)
    Domains in SCOPe 2.08: d2va1c_
  • Chain 'D':
    Compound: uridylate kinase
    Species: Ureaplasma parvum [TaxId:134821]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VA1
    • Uniprot Q9PPX6 (21-255)
    Domains in SCOPe 2.08: d2va1d_
  • Chain 'E':
    Compound: uridylate kinase
    Species: Ureaplasma parvum [TaxId:134821]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VA1
    • Uniprot Q9PPX6 (21-255)
    Domains in SCOPe 2.08: d2va1e_
  • Chain 'F':
    Compound: uridylate kinase
    Species: Ureaplasma parvum [TaxId:134821]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VA1
    • Uniprot Q9PPX6 (Start-255)
    Domains in SCOPe 2.08: d2va1f_
  • Heterogens: PO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2va1A (A:)
    mgsshhhhhhssglvprgshmmrkqrivikisgaclkqndssiidfikindlaeqiekis
    kkyivsivlgggniwrgsiakeldmdrnladnmgmmatiinglalenalnhlnvntivls
    aikcdklvhessannikkaiekeqvmifvagtgfpyfttdscaairaaetessiilmgkn
    gvdgvydsdpkinpnaqfyehitfnmaltqnlkvmdatalalcqenninllvfnidkpna
    ivdvlekknkytivsk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2va1A (A:)
    rkqrivikisgaclkqndssiidfikindlaeqiekiskkyivsivlgggniwrgsiake
    ldmdrnladnmgmmatiinglalenalnhlnvntivlsaikcdklvhessannikkaiek
    eqvmifvagtgfpyfttdscaairaaetessiilmgkngvdgvydsdfyehitfnmaltq
    nlkvmdatalalcqenninllvfnidkpnaivdvlekknkytivsk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2va1B (B:)
    mgsshhhhhhssglvprgshmmrkqrivikisgaclkqndssiidfikindlaeqiekis
    kkyivsivlgggniwrgsiakeldmdrnladnmgmmatiinglalenalnhlnvntivls
    aikcdklvhessannikkaiekeqvmifvagtgfpyfttdscaairaaetessiilmgkn
    gvdgvydsdpkinpnaqfyehitfnmaltqnlkvmdatalalcqenninllvfnidkpna
    ivdvlekknkytivsk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2va1B (B:)
    prgshmmrkqrivikisgaclkqndssiidfikindlaeqiekiskkyivsivlgggniw
    rgsiakeldmdrnladnmgmmatiinglalenalnhlnvntivlsaikcdklvhessann
    ikkaiekeqvmifvagtgfpyfttdscaairaaetessiilmgkngvdgvydpnaqfyeh
    itfnmaltqnlkvmdatalalcqenninllvfnidkpnaivdvlekknkytivsk
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2va1C (C:)
    mgsshhhhhhssglvprgshmmrkqrivikisgaclkqndssiidfikindlaeqiekis
    kkyivsivlgggniwrgsiakeldmdrnladnmgmmatiinglalenalnhlnvntivls
    aikcdklvhessannikkaiekeqvmifvagtgfpyfttdscaairaaetessiilmgkn
    gvdgvydsdpkinpnaqfyehitfnmaltqnlkvmdatalalcqenninllvfnidkpna
    ivdvlekknkytivsk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2va1C (C:)
    kqrivikisgaclkqndssiidfikindlaeqiekiskkyivsivlgggniwrgsiakel
    dmdrnladnmgmmatiinglalenalnhlnvntivlsaikcdklvhessannikkaieke
    qvmifvagtgfpyfttdscaairaaetessiilmgkngvdgvydsdaqfyehitfnmalt
    qnlkvmdatalalcqenninllvfnidkpnaivdvlekknkytivsk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2va1D (D:)
    mgsshhhhhhssglvprgshmmrkqrivikisgaclkqndssiidfikindlaeqiekis
    kkyivsivlgggniwrgsiakeldmdrnladnmgmmatiinglalenalnhlnvntivls
    aikcdklvhessannikkaiekeqvmifvagtgfpyfttdscaairaaetessiilmgkn
    gvdgvydsdpkinpnaqfyehitfnmaltqnlkvmdatalalcqenninllvfnidkpna
    ivdvlekknkytivsk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2va1D (D:)
    mrkqrivikisgaclkqndssiidfikindlaeqiekiskkyivsivlgggniwrgsiak
    eldmdrnladnmgmmatiinglalenalnhlnvntivlsaikcdklvhessannikkaie
    keqvmifvagtgfpyfttdscaairaaetessiilmgkngvdgvydsaqfyehitfnmal
    tqnlkvmdatalalcqenninllvfnidkpnaivdvlekknkytivsk
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2va1E (E:)
    mgsshhhhhhssglvprgshmmrkqrivikisgaclkqndssiidfikindlaeqiekis
    kkyivsivlgggniwrgsiakeldmdrnladnmgmmatiinglalenalnhlnvntivls
    aikcdklvhessannikkaiekeqvmifvagtgfpyfttdscaairaaetessiilmgkn
    gvdgvydsdpkinpnaqfyehitfnmaltqnlkvmdatalalcqenninllvfnidkpna
    ivdvlekknkytivsk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2va1E (E:)
    mrkqrivikisgaclkqndssiidfikindlaeqiekiskkyivsivlgggniwrgsiak
    eldmdrnladnmgmmatiinglalenalnhlnvntivlsaikcdklvhessannikkaie
    keqvmifvagtgfpyfttdscaairaaetessiilmgkngvdgvydsdpkinpnaqfyeh
    itfnmaltqnlkvmdatalalcqenninllvfnidkpnaivdvlekknkytivsk
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2va1F (F:)
    mgsshhhhhhssglvprgshmmrkqrivikisgaclkqndssiidfikindlaeqiekis
    kkyivsivlgggniwrgsiakeldmdrnladnmgmmatiinglalenalnhlnvntivls
    aikcdklvhessannikkaiekeqvmifvagtgfpyfttdscaairaaetessiilmgkn
    gvdgvydsdpkinpnaqfyehitfnmaltqnlkvmdatalalcqenninllvfnidkpna
    ivdvlekknkytivsk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2va1F (F:)
    rkqrivikisgaclkqndssiidfikindlaeqiekiskkyivsivlgggniwrgsiake
    ldmdrnladnmgmmatiinglalenalnhlnvntivlsaikcdklvhessannikkaiek
    eqvmifvagtgfpyfttdscaairaaetessiilmgkngvdgvydsqfyehitfnmaltq
    nlkvmdatalalcqenninllvfnidkpnaivdvlekknkytivsk