5D3G
Structure of HIV-1 Reverse Transcriptase Bound to a Novel 38-mer Hairpin Template-Primer DNA Aptamer
- PDB DOI: https://doi.org/10.2210/pdb5D3G/pdb
- NAKB: 5D3G
- Classification: TRANSFERASE
- Organism(s): Human immunodeficiency virus type 1 BH10, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2015-08-06 Released: 2015-09-30 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.225 
- R-Value Work: 0.191 
- R-Value Observed: 0.191 
wwPDB Validation   3D Report Full Report
This is version 3.1 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 | 555 | Human immunodeficiency virus type 1 BH10 | Mutation(s): 1  Gene Names: gag-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% 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 type 1 BH10 | Mutation(s): 1  Gene Names: gag-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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P03366 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
DNA aptamer (38-MER) | E [auth F], F [auth E] | 38 | synthetic construct | ||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | I [auth A], P [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | J [auth A] K [auth B] L [auth B] M [auth B] N [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.30 Å
- R-Value Free: 0.225 
- R-Value Work: 0.191 
- R-Value Observed: 0.191 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 90.015 | α = 90 |
b = 128.907 | β = 101.34 |
c = 132.615 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-09-30  Deposition Author(s): 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 | GM103368 |
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI027690 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM1033 |
Revision History (Full details and data files)
- Version 1.0: 2015-09-30
Type: Initial release - Version 1.1: 2016-01-13
Changes: Database references - Version 1.2: 2017-09-20
Changes: Author supporting evidence, Database references, Derived calculations - Version 2.0: 2019-07-31
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Structure summary - Version 2.1: 2019-08-14
Changes: Data collection, Derived calculations - Version 2.2: 2019-12-11
Changes: Author supporting evidence - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 3.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary