2B6A | pdb_00002b6a

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with THR-50

PDB DOI: https://doi.org/10.2210/pdb2B6A/pdb

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

Deposited: 2005-09-30 Released: 2005-11-01
Deposition Author(s): Morningstar, M.L., Roth, T., Smith, M.K., Zajac, M., Watson, K., Buckheit, R.W., Das, K., Zhang, W., Arnold, E., Michejda, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.277 (Depositor), 0.236 (DCC)
R-Value Work:
0.226 (Depositor), 0.227 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with THR-50

Morningstar, M.L., Roth, T., Smith, M.K., Zajac, M., Watson, K., Buckheit, R.W., Das, K., Zhang, W., Arnold, E., Michejda, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 115.15 kDa
Atom Count: 7,921
Modeled Residue Count: 985
Deposited Residue Count: 990
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase p66 subunit	A	560	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: POL 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase p51 subunit	B	430	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: POL 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 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
T50 Query on T50 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1-(2,6-DIFLUOROBENZYL)-2-(2,6-DIFLUOROPHENYL)-4-METHYL-1H-BENZIMIDAZOLE C₂₁ H₁₄ F₄ N₂ JIYRSPUMGRIYBL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.277 (Depositor), 0.236 (DCC)
R-Value Work: 0.226 (Depositor), 0.227 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 227.706	α = 90
b = 70.168	β = 105.82
c = 106.63	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-11-01

Deposition Author(s):

Morningstar, M.L.

Revision History (Full details and data files)

Version 1.0: 2005-11-01
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: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-08-23
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.