3ITH

Crystal structure of the HIV-1 reverse transcriptase bound to a 6-vinylpyrimidine inhibitor

PDB DOI: https://doi.org/10.2210/pdb3ITH/pdb

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

Deposited: 2009-08-28 Released: 2010-03-16
Deposition Author(s): Freisz, S., Bec, G., Wolff, P., Dumas, P., Radi, M., Botta, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.270
R-Value Work: 0.212
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

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 of 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: 229.34 kDa
Atom Count: 15,912
Modelled Residue Count: 1,942
Deposited Residue Count: 1,974
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A, 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p51 RT	B, 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 E [auth A] SDF format, chain F [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C]	E [auth A], F [auth C]	6-ethenyl-N,N-dimethyl-2-(methylsulfonyl)pyrimidin-4-amine C₉ H₁₃ N₃ O₂ S LWXYVFFCCMAZFC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
EDM	PDBBind: 3ITH	Ki: 8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.270
R-Value Work: 0.212
R-Value Observed: 0.215
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.1	α = 90
b = 72.49	β = 95.89
c = 216.29	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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: 2014-04-16
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description