Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 131187.19 
• Atom Count: 8877 
• Residue Count: 1043 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

1T05

HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate

• DOI: 10.2210/pdb1T05/pdb
• NDB: PD0537

• Classification: Transferase/DNA
• Organism(s): Human immunodeficiency virus type 1 group M subtype B (isolate BH10), Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2004-04-07 Released: 2004-05-11 
• Deposition Author(s): Tuske, S., Sarafianos, S.G., Ding, J., Arnold, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.292 
• R-Value Work: 0.253 

Literature

Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir

Tuske, S., Sarafianos, S.G., Clark Jr., A.D., Ding, J., Naeger, L.K., White, K.L., Miller, M.D., Gibbs, C.S., Boyer, P.L., Clark, P., Wang, G., Gaffney, B.L., Jones, R.A., Jerina, D.M., Hughes, S.H., Arnold, E.

(2004) Nat.Struct.Mol.Biol. 11: 469-474

• PubMed: 15107837 
• DOI: 10.1038/nsmb760
• Primary Citation of Related Structures:  
  1T03
• Also Cited By: 3JYT, 3JSM


• PubMed Abstract: 
  

Tenofovir, also known as PMPA, R-9-(2-(phosphonomethoxypropyl)adenine, is a nucleotide reverse transcriptase (RT) inhibitor. We have determined the crystal structures of two related complexes of HIV-1 RT with template primer and tenofovir: (i) a ternary complex at a resolution of 3.0 A of RT crosslinked to a dideoxy-terminated DNA with tenofovir-diphosphate bound as the incoming substrate; and (ii) a RT-DNA complex at a resolution of 3.1 A with tenofovir at the 3' primer terminus. The tenofovir nucleotide in the tenofovir-terminated structure seems to adopt multiple conformations. Some nucleoside reverse transcriptase inhibitors, including 3TC and AZT, have elements ('handles') that project beyond the corresponding elements on normal dNTPs (the 'substrate envelope'). HIV-1 RT resistance mechanisms to AZT and 3TC take advantage of these handles; tenofovir's structure lacks handles that could protrude through the substrate envelope to cause resistance.

---

Organizational Affiliation: 

Center for Advanced Biotechnology and Medicine and Rutgers University Department of Chemistry and Chemical Biology, 679 Hoes Lane, Piscataway, New Jersey 08854-5638, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
POL polyprotein	A	558	Human immunodeficiency virus type 1 group M subtype B (isolate BH10)	Mutation(s): 2  Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Go to UniProtKB:  P03366

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
POL polyprotein	B	437	Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)	Mutation(s): 1  Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Go to UniProtKB:  P04585

Entity ID: 1
Molecule	Chains	Length	Organism
oligonucleotide template	T	27	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
oligonucleotide primer	P	21	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TNV	A	[2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE TENOFOVIR-DIPHOSPHATE C9 H16 N5 O10 P3 IACQCQDWSIQSRP-ZCFIWIBFSA-N
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DDG	P	DNA LINKING	C10 H14 N5 O6 P		DG
MRG	P	DNA LINKING	C13 H20 N5 O7 P S		DG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.292 
• R-Value Work: 0.253 
• Space Group: P 3₁ 1 2

Unit Cell:

Length (Å)	Angle (°)
a = 171.570	α = 90.00
b = 171.570	β = 90.00
c = 156.270	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	phasing
DENZO	data reduction
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-07 
• Released Date: 2004-05-11 
• Deposition Author(s): Tuske, S., Sarafianos, S.G., Ding, J., Arnold, E.

Revision History 

• Version 1.0: 2004-05-11
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance