6BHJ
Structure of HIV-1 Reverse Transcriptase Bound to a 38-mer Hairpin Template-Primer RNA-DNA Aptamer
- PDB DOI: https://doi.org/10.2210/pdb6BHJ/pdb
- NAKB: 6BHJ
- Classification: TRANSFERASE/DNA
- Organism(s): Human immunodeficiency virus 1, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2017-10-30 Released: 2018-10-31 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.81 Å
- R-Value Free: 0.244 
- R-Value Work: 0.203 
- R-Value Observed: 0.205 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HIV-1 REVERSE TRANSCRIPTASE P66 subunit | 557 | Human immunodeficiency virus 1 | Mutation(s): 3  Gene Names: pol | ||
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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HIV-1 REVERSE TRANSCRIPTASE P51 subunit | 444 | Human immunodeficiency virus 1 | Mutation(s): 2  Gene Names: pol | ||
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 AnnotationsExpand | |||||
|
Find similar nucleic acids by: 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
38-MER RNA-DNA Aptamer | 38 | synthetic construct | |||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | N [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | J [auth B] K [auth B] L [auth B] M [auth B] O [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
MG Query on MG | I [auth A], P [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900003 Query on PRD_900003 | G, H | sucrose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.81 Å
- R-Value Free: 0.244 
- R-Value Work: 0.203 
- R-Value Observed: 0.205 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 90.055 | α = 90 |
b = 127.463 | β = 101.81 |
c = 132.125 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data processing |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-10-31  Deposition Author(s): Ruiz, F.X., Miller, M.T., Tuske, S., Das, K., Arnold, E.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | NIGMS P50 GM103368 |
Revision History (Full details and data files)
- Version 1.0: 2018-10-31
Type: Initial release - Version 1.1: 2019-02-20
Changes: Advisory, Author supporting evidence, Data collection, Derived calculations - Version 1.2: 2020-01-01
Changes: Author supporting evidence - Version 1.3: 2020-07-08
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary