2I5J

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with DHBNH, an RNASE H inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2I5J/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-08-24 Released: 2006-12-05 
• Deposition Author(s): Himmel, D.M., Sarafianos, S.G., Knight, J.L., Levy, R.M., Arnold, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.269 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 115.4 kDa 
• Atom Count: 8,108 
• Modelled Residue Count: 972 
• Deposited Residue Count: 981 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H P66 subunit	A	552	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: gag EC: 2.7.7.49
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H P51 subunit	B	429	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: gag EC: 2.7.7.49
UniProt
Find proteins for Q8UM83 (Human immunodeficiency virus 1) Explore Q8UM83  Go to UniProtKB:  Q8UM83

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K05	G [auth A]	(E)-3,4-DIHYDROXY-N'-[(2-METHOXYNAPHTHALEN-1-YL)METHYLENE]BENZOHYDRAZIDE C19 H16 N2 O4 TVOPERZEGKBKAY-RGVLZGJSSA-N
GLC	E [auth A], F [auth A], I [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
MG	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
K05	BindingDB:  2I5J	IC50: min: 500, max: 2.50e+4 (nM) from 8 assay(s)
	PDBBind:  2I5J	IC50: 500 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C, D	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.269 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.815	α = 90
b = 68.896	β = 106.48
c = 104.662	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Himmel, D.M., Sarafianos, S.G., Knight, J.L., Levy, R.M., Arnold, E.

Revision History  

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-08-30
  Changes: Data collection, Refinement description