3KLE

Crystal structure of AZT-resistant HIV-1 Reverse Transcriptase crosslinked to a DSDNA with a bound excision product, AZTPPPPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.308 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.280 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.280 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

Structural basis of HIV-1 resistance to AZT by excision.

Tu, X.Das, K.Han, Q.Bauman, J.D.Clark, A.D.Hou, X.Frenkel, Y.V.Gaffney, B.L.Jones, R.A.Boyer, P.L.Hughes, S.H.Sarafianos, S.G.Arnold, E.

(2010) Nat Struct Mol Biol 17: 1202-1209

  • DOI: https://doi.org/10.1038/nsmb.1908
  • Primary Citation of Related Structures:  
    3KLE, 3KLF, 3KLG, 3KLH, 3KLI

  • PubMed Abstract: 

    Human immunodeficiency virus (HIV-1) develops resistance to 3'-azido-2',3'-deoxythymidine (AZT, zidovudine) by acquiring mutations in reverse transcriptase that enhance the ATP-mediated excision of AZT monophosphate from the 3' end of the primer. The excision reaction occurs at the dNTP-binding site, uses ATP as a pyrophosphate donor, unblocks the primer terminus and allows reverse transcriptase to continue viral DNA synthesis. The excision product is AZT adenosine dinucleoside tetraphosphate (AZTppppA). We determined five crystal structures: wild-type reverse transcriptase-double-stranded DNA (RT-dsDNA)-AZTppppA; AZT-resistant (AZTr; M41L D67N K70R T215Y K219Q) RT-dsDNA-AZTppppA; AZTr RT-dsDNA terminated with AZT at dNTP- and primer-binding sites; and AZTr apo reverse transcriptase. The AMP part of AZTppppA bound differently to wild-type and AZTr reverse transcriptases, whereas the AZT triphosphate part bound the two enzymes similarly. Thus, the resistance mutations create a high-affinity ATP-binding site. The structure of the site provides an opportunity to design inhibitors of AZT-monophosphate excision.


  • Organizational Affiliation

    Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse transcriptase/ribonuclease HA,
C [auth E],
E [auth I],
G [auth M]
562Human immunodeficiency virus type 1 BH10Mutation(s): 7 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
p51 RTB,
D [auth F],
F [auth J],
H [auth N]
437Human immunodeficiency virus type 1 BH10Mutation(s): 1 
Gene Names: gag-pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Q
2N/A
Glycosylation Resources
GlyTouCan:  G49187ZK
GlyCosmos:  G49187ZK
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZP4
Query on ZP4

Download Ideal Coordinates CCD File 
BA [auth I],
EA [auth M],
T [auth A],
X [auth E]
[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen phosphate
C20 H28 N10 O19 P4
NHJROJSMKQZWCP-SLFMBYJQSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
U [auth B],
Y [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth I]
CA [auth M]
DA [auth M]
R [auth A]
S [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.308 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.280 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.280 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.738α = 90
b = 283.33β = 89.73
c = 155.233γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ZP4Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-10-13
    Changes: Database references, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Data collection, Structure summary