5XN2

HIV-1 reverse transcriptase Q151M:DNA:dGTP ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.381 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir.

Yasutake, Y.Hattori, S.I.Hayashi, H.Matsuda, K.Tamura, N.Kohgo, S.Maeda, K.Mitsuya, H.

(2018) Sci Rep 8: 1624-1624


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pol protein
A, C
557Human immunodeficiency virus type 1 group M subtype BMutation(s): 3 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12497
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pol protein
B, D
444Human immunodeficiency virus type 1 group M subtype BMutation(s): 2 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12497
Entity ID: 3
MoleculeChainsLengthOrganism
38-MER DNA aptamerE,F38synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
B
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DGT
Query on DGT

Download SDF File 
Download CCD File 
A, C
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMC
Query on OMC
E, F
RNA LINKINGC10 H16 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.381 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 285.694α = 90.00
b = 285.694β = 90.00
c = 96.325γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
MOLREPphasing
XDSdata processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release