General information
PDB ID 1RTD
Title STRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: IMPLICATIONS FOR NUCLEOSIDE ANALOG DRUG RESISTANCE
PDB header TRANSFERASE/DNA
Date 1998-08-26
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.2
Kind dna
Organism HUMAN IMMUNODEFICIENCY VIRUS 1
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb1rtd.pdb ABCD EFGH 0
Biounits:
1rtd.pdb1.pdb AB EF 1
1rtd.pdb2.pdb CD GH 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
RVT_connect Domain P03366_917-1018 2.5e-59 1 No_clan A 318 419 EF  H-Bb S-Bb L-Bb 
RVT_1 Domain P03366_662-833 7.3e-35 1 CL0027 A 63 234 FE  H-Bb S-Bb S-Mn L-Bb L-Mn 
RNase_H Domain P03366_1035-1153 1.4e-26 1 CL0219 A 436 554 EF  H-Bb L-Bb L-Mn 
RVT_thumb Domain P03366_840-903 4.3e-21 1 No_clan A 241 304 EF  H-Bb L-Bb 
RVT_connect Domain P04585_905-1006 1.5e-59 1 No_clan B 318 419   
RVT_1 Domain P04585_650-821 3.7e-33 1 CL0027 B 63 243   
RVT_thumb Domain P04585_828-891 5.5e-23 1 No_clan B 241 304   
RVT_connect Domain P03366_917-1018 2.5e-59 1 No_clan C 318 419 GH  H-Bb S-Bb 
RVT_1 Domain P03366_662-833 7.3e-35 1 CL0027 C 63 234 HG  H-Bb S-Bb S-Mn L-Bb L-Mn 
RNase_H Domain P03366_1035-1153 1.4e-26 1 CL0219 C 436 554 GH  H-Bb H-Mn L-Bb L-Mn 
RVT_thumb Domain P03366_840-903 4.3e-21 1 No_clan C 241 304 GH  H-Bb L-Bb 
RVT_connect Domain P04585_905-1006 1.5e-59 1 No_clan D 318 419 H  H-Bb 
RVT_1 Domain P04585_650-821 3.7e-33 1 CL0027 D 63 243   
RVT_thumb Domain P04585_828-891 5.5e-23 1 No_clan D 241 304   
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: Alpha and beta proteins (a/b)
  Fold: Ribonuclease H-like motif
    Superfamily: Ribonuclease H-like
      Family: Ribonuclease H
HIV RNase H (Domain of reverse transcriptase) A 430 554 EF -
Class: Alpha and beta proteins (a/b)
  Fold: Ribonuclease H-like motif
    Superfamily: Ribonuclease H-like
      Family: Ribonuclease H
HIV RNase H (Domain of reverse transcriptase) C 430 554 GH -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: Reverse transcriptase
HIV-1 reverse transcriptase A 1 429 EF -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: Reverse transcriptase
HIV-1 reverse transcriptase B N/A N/A -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: Reverse transcriptase
HIV-1 reverse transcriptase C 1 429 GH -
Class: Multi-domain proteins (alpha and beta)
  Fold: DNA/RNA polymerases
    Superfamily: DNA/RNA polymerases
      Family: Reverse transcriptase
HIV-1 reverse transcriptase D N/A N/A H -
GO terms
Protein chains: GO type: GO description:
A/C=600-1153 C host cell nucleus
A/C=600-1153 C host cell plasma membrane
A/C=600-1153 C host multivesicular body
A/C=600-1153 C viral nucleocapsid
A/C=600-1153 C virion membrane
A/C=600-1153 F aspartic-type endopeptidase activity
A/C=600-1153 F DNA binding
A/C=600-1153 F DNA-directed DNA polymerase activity
A/C=600-1153 F exoribonuclease H activity
A/C=600-1153 F lipid binding
A/C=600-1153 F RNA binding
A/C=600-1153 F RNA-directed DNA polymerase activity
A/C=600-1153 F RNA-DNA hybrid ribonuclease activity
A/C=600-1153 F structural molecule activity
A/C=600-1153 F zinc ion binding
A/C=600-1153 P DNA integration
A/C=600-1153 P DNA recombination
A/C=600-1153 P establishment of integrated proviral latency
A/C=600-1153 P induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process
A/C=600-1153 P suppression by virus of host gene expression
A/C=600-1153 P viral entry into host cell
A/C=600-1153 P viral genome integration into host DNA
A/C=600-1153 P viral penetration into host nucleus
B/D=588-1027 C host cell nucleus
B/D=588-1027 C host cell plasma membrane
B/D=588-1027 C host multivesicular body
B/D=588-1027 C viral nucleocapsid
B/D=588-1027 C virion membrane
B/D=588-1027 F aspartic-type endopeptidase activity
B/D=588-1027 F DNA binding
B/D=588-1027 F DNA-directed DNA polymerase activity
B/D=588-1027 F exoribonuclease H activity
B/D=588-1027 F identical protein binding
B/D=588-1027 F integrase activity
B/D=588-1027 F lipid binding
B/D=588-1027 F peptidase activity
B/D=588-1027 F RNA binding
B/D=588-1027 F RNA-directed DNA polymerase activity
B/D=588-1027 F RNA-DNA hybrid ribonuclease activity
B/D=588-1027 F structural molecule activity
B/D=588-1027 F zinc ion binding
B/D=588-1027 P DNA recombination
B/D=588-1027 P establishment of integrated proviral latency
B/D=588-1027 P fusion of virus membrane with host plasma membrane
B/D=588-1027 P induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process
B/D=588-1027 P nuclear transport
B/D=588-1027 P RNA-dependent DNA biosynthetic process
B/D=588-1027 P suppression by virus of host gene expression
B/D=588-1027 P uncoating of virus
B/D=588-1027 P viral genome integration into host DNA
B/D=588-1027 P viral genome packaging
B/D=588-1027 P viral life cycle
B/D=588-1027 P viral penetration into host nucleus
B/D=588-1027 P virion assembly
Sequences
Download file with secondary structure created by Stride  
1rtd.pdb1.pdb:   [ download sequences in FASTA format ]
E (dna): 
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F (dna): 
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A (protein): 
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B (protein): 
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1rtd.pdb2.pdb:   [ download sequences in FASTA format ]
G (dna): 
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H (dna): 
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C (protein): 
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D (protein): 
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