3HYF | pdb_00003hyf

Crystal structure of HIV-1 RNase H p15 with engineered E. coli loop and active site inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3HYF/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-22 Released: 2009-10-20 
• Deposition Author(s): Lansdon, E.B., Kirschberg, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.232 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

RNase H active site inhibitors of human immunodeficiency virus type 1 reverse transcriptase: design, biochemical activity, and structural information.

Kirschberg, T.A., Balakrishnan, M., Squires, N.H., Barnes, T., Brendza, K.M., Chen, X., Eisenberg, E.J., Jin, W., Kutty, N., Leavitt, S., Liclican, A., Liu, Q., Liu, X., Mak, J., Perry, J.K., Wang, M., Watkins, W.J., Lansdon, E.B.

(2009) J Med Chem 52: 5781-5784

• PubMed: 19791799 
• DOI: https://doi.org/10.1021/jm900597q
• Primary Citation Related Structures: 
  3HYF


• PubMed Abstract: 
  

  Pyrimidinol carboxylic acids were designed as inhibitors of HIV-1 RNase H function. These molecules can coordinate to two divalent metal ions in the RNase H active site. Inhibition of enzymatic activity was measured in a biochemical assay, but no antiviral effect was observed. Binding was demonstrated via a solid state structure of the isolated p15-Ec domain of HIV-1 RT showing inhibitor and two Mn(II) ions bound to the RNase H active site.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Gilead Sciences, Foster City, California 94404, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.59 kDa 
• Atom Count: 1,370 
• Modeled Residue Count: 143 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/RNaseH	A	150	Human immunodeficiency virus 1, Escherichia coli K-12	Mutation(s): 0  Gene Names: pol, Reverse Transcriptase (amino acids 427-560) EC: 3.1.26.4
UniProt
Find proteins for P0A7Y4 (Escherichia coli (strain K12)) Explore P0A7Y4  Go to UniProtKB:  P0A7Y4
Find proteins for Q72547 (Human immunodeficiency virus type 1) Explore Q72547  Go to UniProtKB:  Q72547
UniProt Groups	Q72547P0A7Y4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ON1	G [auth A]	2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid C12 H8 Cl2 N2 O4 OZDSTVKQUHMIRA-UHFFFAOYSA-N
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.232 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.717	α = 90
b = 90.326	β = 90
c = 113.334	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
AMoRE	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Lansdon, E.B., Kirschberg, T.A.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-03-13
  Changes: Source and taxonomy