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
Deposition Author(s): Miller, M.T., Tuske, S., Das, K., Arnold, E.
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.

Macromolecule Content

Total Structure Weight: 256.99 kDa
Atom Count: 17,868
Modelled Residue Count: 2,003
Deposited Residue Count: 2,074
Unique protein chains: 2
Unique nucleic acid chains: 1

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	A, C	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 Annotations Expand
Reference Sequence

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	B, D	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 Annotations Expand
Reference Sequence

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 Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	G, H	2		N/A	Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain I [auth A]	I [auth A], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain P [auth C] Interactions & Density Focus chain I [auth A] Focus chain P [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain T [auth D] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain U [auth F] MOL2 format, chain N [auth B] MOL2 format, chain T [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth F]	J [auth A] K [auth B] L [auth B] M [auth B] N [auth B] J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth D], S [auth D], T [auth D], U [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth F] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth F]

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		Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H

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 Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-09-30

Deposition Author(s):

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