PDB entry 4pwd

View 4pwd on RCSB PDB site
Description: Crystal structure of HIV-1 reverse transcriptase in complex with bulge-RNA/DNA and Nevirapine
Class: transferase, hydrolase/DNA/RNA/inhibitor
Keywords: fingers, palm, thumb, connection, RNase H, nucleotidyltransferase, DNA-directed DNA polymerase, RNA-directed DNA polymerase, nuclease, Ribonuclease H, tRNA, TRANSFERASE, HYDROLASE-DNA-RNA-INHIBITOR complex
Deposited on 2014-03-19, released 2014-06-18
The last revision prior to the SCOPe 2.06 freeze date was dated 2014-07-16, with a file datestamp of 2014-07-11.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.223
AEROSPACI score: 0.15 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: HIV-1 reverse transcriptase, p66 subunit
    Species: Human immunodeficiency virus type 1 [TaxId:11678]
    Gene: gag-pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03366 (2-555)
      • expression tag (1)
      • engineered mutation (259)
      • engineered mutation (281)
      • engineered mutation (499)
    Domains in SCOPe 2.06: d4pwda1, d4pwda2, d4pwda3
  • Chain 'B':
    Compound: HIV-1 reverse transcriptase, p51 subunit
    Species: Human immunodeficiency virus type 1 [TaxId:11678]
    Gene: gag-pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03366 (Start-427)
      • engineered mutation (279)
    Domains in SCOPe 2.06: d4pwdb_
  • Chain 'C':
    Compound: HIV-1 reverse transcriptase, p66 subunit
    Species: Human immunodeficiency virus type 1 [TaxId:11678]
    Gene: gag-pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03366 (2-555)
      • expression tag (1)
      • engineered mutation (259)
      • engineered mutation (281)
      • engineered mutation (499)
    Domains in SCOPe 2.06: d4pwdc1, d4pwdc2, d4pwdc3
  • Chain 'D':
    Compound: HIV-1 reverse transcriptase, p51 subunit
    Species: Human immunodeficiency virus type 1 [TaxId:11678]
    Gene: gag-pol
    Database cross-references and differences (RAF-indexed):
    • Uniprot P03366 (Start-427)
      • engineered mutation (279)
    Domains in SCOPe 2.06: d4pwdd_
  • Chain 'E':
    Compound: 5'-r(*ap*up*gp*gp*up*cp*gp*gp*cp*gp*cp*cp*cp*gp*ap*ap*ap*cp*ap*gp*gp*gp*ap*cp*up*gp*u)-3'
  • Chain 'F':
    Compound: 5'-d(*a*cp*ap*gp*tp*cp*cp*cp*tp*gp*tp*tp*cp*gp*gp*gp*cp*gp*cp*cp*g)-3'
  • Chain 'P':
    Compound: 5'-d(*a*cp*ap*gp*tp*cp*cp*cp*tp*gp*tp*tp*cp*gp*gp*gp*cp*gp*cp*cp*g)-3'
  • Chain 'T':
    Compound: 5'-r(*ap*up*gp*gp*up*cp*gp*gp*cp*gp*cp*cp*cp*gp*ap*ap*ap*cp*ap*gp*gp*gp*ap*cp*up*gp*u)-3'
  • Heterogens: NVP, CA, SO4

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4pwdA (A:)
    mvpispietvpvklkpgmdgpkvkqwplteekikalveictemekegkiskigpenpynt
    pvfaikkkdstkwrklvdfrelnkrtqdfwevqlgiphpaglkkkksvtvldvgdayfsv
    pldedfrkytaftipsinnetpgiryqynvlpqgwkgspaifqssmtkilepfkkqnpdi
    viyqymddlyvgsdleigqhrtkieelrqhllrwglttpdkkhqkeppflwmgyelhpdk
    wtvqpivlpekdswtvndicklvgklnwasqiypgikvrqlskllrgtkaltevipltee
    aelelaenreilkepvhgvyydpskdliaeiqkqgqgqwtyqiyqepfknlktgkyarmr
    gahtndvkqlteavqkittesiviwgktpkfklpiqketwetwwteywqatwipewefvn
    tpplvklwyqlekepivgaetfyvdgaanretklgkagyvtnkgrqkvvpltnttnqkte
    lqaiylalqdsglevnivtnsqyalgiiqaqpdkseselvnqiieqlikkekvylawvpa
    hkgiggneqvdklvsa
    

    Sequence, based on observed residues (ATOM records): (download)
    >4pwdA (A:)
    vpispietvpvklkpgmdgpkvkqwplteekikalveictemekegkiskigpenpyntp
    vfaikkkdstkwrklvdfrelnkrtqdfwevqlgiphpaglkkkksvtvldvgdayfsvp
    ldedfrkytaftipsinnetpgiryqynvlpqgwkgspaifqssmtkilepfkkqnpdiv
    iyqymddlyvgsdleigqhrtkieelrqhllrwglttpdkkhqkeppflwmgyelhpdkw
    tvqpivlpekdswtvndicklvgklnwasqiypgikvrqlskllrgtkalteviplteea
    elelaenreilkepvhgvyydpskdliaeiqkqgqgqwtyqiyqepfknlktgkyarmrg
    ahtndvkqlteavqkittesiviwgktpkfklpiqketwetwwteywqatwipewefvnt
    pplvklwyqlekepivgaetfyvdgaanretklgkagyvtnkgrqkvvpltnttnqktel
    qaiylalqdsglevnivtnsqyalgiiqaqpdkseselvnqiieqlikkekvylawvpah
    kgiggneqvdklvsa
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4pwdB (B:)
    pispietvpvklkpgmdgpkvkqwplteekikalveictemekegkiskigpenpyntpv
    faikkkdstkwrklvdfrelnkrtqdfwevqlgiphpaglkkkksvtvldvgdayfsvpl
    dedfrkytaftipsinnetpgiryqynvlpqgwkgspaifqssmtkilepfkkqnpdivi
    yqymddlyvgsdleigqhrtkieelrqhllrwglttpdkkhqkeppflwmgyelhpdkwt
    vqpivlpekdswtvndiqklvgklnwasqiypgikvrqlskllrgtkalteviplteeae
    lelaenreilkepvhgvyydpskdliaeiqkqgqgqwtyqiyqepfknlktgkyarmrga
    htndvkqlteavqkittesiviwgktpkfklpiqketwetwwteywqatwipewefvntp
    plvklwyq
    

    Sequence, based on observed residues (ATOM records): (download)
    >4pwdB (B:)
    pietvpvklkpgmdgpkvkqwplteekikalveictemekegkiskigpenpyntpvfai
    kkkdstkwrklvdfrelnkrtqdfwevqlgiphpaglkkkksvtvldvgdayfsvplded
    frkytaftipsinnetpgiryqynvlpqgwkgspaifqssmtkilepfkkqnpdiviyqy
    mddlyvgsdleigqhrtkieelrqhllrwglttpgyelhpdkwtvqpivlpekdswtvnd
    iqklvgklnwasqiypgikvrqlskllrgtkalteviplteeaelelaenreilkepvhg
    vyydpskdliaeiqkqgqgqwtyqiyqepfknlktgkyarmrgahtndvkqlteavqkit
    tesiviwgktpkfklpiqketwetwwteywqatwipewefvntpplvklwyq
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4pwdC (C:)
    mvpispietvpvklkpgmdgpkvkqwplteekikalveictemekegkiskigpenpynt
    pvfaikkkdstkwrklvdfrelnkrtqdfwevqlgiphpaglkkkksvtvldvgdayfsv
    pldedfrkytaftipsinnetpgiryqynvlpqgwkgspaifqssmtkilepfkkqnpdi
    viyqymddlyvgsdleigqhrtkieelrqhllrwglttpdkkhqkeppflwmgyelhpdk
    wtvqpivlpekdswtvndicklvgklnwasqiypgikvrqlskllrgtkaltevipltee
    aelelaenreilkepvhgvyydpskdliaeiqkqgqgqwtyqiyqepfknlktgkyarmr
    gahtndvkqlteavqkittesiviwgktpkfklpiqketwetwwteywqatwipewefvn
    tpplvklwyqlekepivgaetfyvdgaanretklgkagyvtnkgrqkvvpltnttnqkte
    lqaiylalqdsglevnivtnsqyalgiiqaqpdkseselvnqiieqlikkekvylawvpa
    hkgiggneqvdklvsa
    

    Sequence, based on observed residues (ATOM records): (download)
    >4pwdC (C:)
    vpispietvpvklkpgmdgpkvkqwplteekikalveictemekegkiskigpenpyntp
    vfaikkkdstkwrklvdfrelnkrtqdfwevqlgiphpaglkkkksvtvldvgdayfsvp
    ldedfrkytaftipsinnetpgiryqynvlpqgwkgspaifqssmtkilepfkkqnpdiv
    iyqymddlyvgsdleigqhrtkieelrqhllrwglttpdkkhqkeppflwmgyelhpdkw
    tvqpivlpekdswtvndicklvgklnwasqiypgikvrqlskllrgtkalteviplteea
    elelaenreilkepvhgvyydpskdliaeiqkqgqgqwtyqiyqepfknlktgkyarmrg
    ahtndvkqlteavqkittesiviwgktpkfklpiqketwetwwteywqatwipewefvnt
    pplvklwyqlekepivgaetfyvdgaanretklgkagyvtnkgrqkvvpltnttnqktel
    qaiylalqdsglevnivtnsqyalgiiqaqpdkseselvnqiieqlikkekvylawvpah
    kgiggneqvdklvsa
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4pwdD (D:)
    pispietvpvklkpgmdgpkvkqwplteekikalveictemekegkiskigpenpyntpv
    faikkkdstkwrklvdfrelnkrtqdfwevqlgiphpaglkkkksvtvldvgdayfsvpl
    dedfrkytaftipsinnetpgiryqynvlpqgwkgspaifqssmtkilepfkkqnpdivi
    yqymddlyvgsdleigqhrtkieelrqhllrwglttpdkkhqkeppflwmgyelhpdkwt
    vqpivlpekdswtvndiqklvgklnwasqiypgikvrqlskllrgtkalteviplteeae
    lelaenreilkepvhgvyydpskdliaeiqkqgqgqwtyqiyqepfknlktgkyarmrga
    htndvkqlteavqkittesiviwgktpkfklpiqketwetwwteywqatwipewefvntp
    plvklwyq
    

    Sequence, based on observed residues (ATOM records): (download)
    >4pwdD (D:)
    pietvpvklkpgmdgpkvkqwplteekikalveictemekegkiskigpenpyntpvfai
    kkkdstkwrklvdfrelnkrtqdfwevqlgiphpaglkkkksvtvldvgdayfsvplded
    frkytaftipsinnetpgiryqynvlpqgwkgspaifqssmtkilepfkkqnpdiviyqy
    mddlyvgsdleigqhrtkieelrqhllrwglttpgyelhpdkwtvqpivlpekdswtvnd
    iqklvgklnwasqiypgikvrqlskllrgtkalteviplteeaelelaenreilkepvhg
    vyydpskdliaeiqkqgqgqwtyqiyqepfknlktgkyarmrgahtndvkqlteavqkit
    tesiviwgktpkfklpiqketwetwwteywqatwipewefvntpplvklwyq
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.

  • Chain 'P':
    No sequence available.

  • Chain 'T':
    No sequence available.