3ISN | pdb_00003isn

Crystal structure of HIV-1 RT bound to A 6-vinylpyrimidine inhibitor

PDB DOI: https://doi.org/10.2210/pdb3ISN/pdb

Classification: TRANSFERASE, HYDROLASE
Organism(s): Human immunodeficiency virus type 1 BH10
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-08-26 Released: 2010-03-16
Deposition Author(s): Ennifar, E., Freisz, S., Bec, G., Dumas, P., Botta, M., Radi, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.281 (Depositor), 0.221 (DCC)
R-Value Work:
0.221 (Depositor), 0.219 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of HIV-1 Reverse Transcriptase Bound to a Non-Nucleoside Inhibitor with a Novel Mechanism of Action

Freisz, S., Bec, G., Radi, M., Wolff, P., Crespan, E., Angeli, L., Dumas, P., Maga, G., Botta, M., Ennifar, E.

(2010) Angew Chem Int Ed Engl 49: 1805-1808

PubMed: 20135654 Search on PubMed
DOI: https://doi.org/10.1002/anie.200905651
Primary Citation Related Structures:
3ISN, 3ITH

Organizational Affiliation

Architecture et réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France.

Macromolecule Content

Total Structure Weight: 114.67 kDa
Atom Count: 8,160
Modeled Residue Count: 971
Deposited Residue Count: 987
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A [auth C]	560	Human immunodeficiency virus type 1 BH10	Mutation(s): 0 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p51 RT	B [auth D]	427	Human immunodeficiency virus type 1 BH10	Mutation(s): 0
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDM Query on EDM Download:Ideal Coordinates CCD File SDF format, chain C MOL2 format, chain C mmCIF format, chain C	C	6-ethenyl-N,N-dimethyl-2-(methylsulfonyl)pyrimidin-4-amine C₉ H₁₃ N₃ O₂ S LWXYVFFCCMAZFC-UHFFFAOYSA-N		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.281 (Depositor), 0.221 (DCC)
R-Value Work: 0.221 (Depositor), 0.219 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.121	α = 90
b = 72.182	β = 108.97
c = 93.516	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2025-05-28
Changes: Structure summary