5TXM

STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WITH A DOUBLE STRANDED DNA AND AN INCOMING DDATP

PDB DOI: https://doi.org/10.2210/pdb5TXM/pdb
NAKB: 5TXM

Classification: TRANSFERASE/DNA
Organism(s): Human immunodeficiency virus type 1 BH10, Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-11-17 Released: 2017-04-05
Deposition Author(s): Das, K., Martinez, S.M., Arnold, E.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.223
R-Value Work: 0.184
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 260.19 kDa
Atom Count: 17,950
Modelled Residue Count: 2,023
Deposited Residue Count: 2,066
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Reverse Transcriptase P66 subunit	A, E [auth C]	557	Human immunodeficiency virus type 1 BH10	Mutation(s): 3 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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Reverse Transcriptase P51 subunit	B, F [auth D]	428	Human immunodeficiency virus type 1 BH10	Mutation(s): 1 Gene Names: gag-pol EC: 2.7.7.7
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

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(TPGPGPTPCPGPGPCPGPCPCPCPGPAPAPCPAPGPGPGPAPCPTPG)-3')	C [auth T], G [auth E]	27	Human immunodeficiency virus 1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPAPGPTPCPCPCPTPGPTPTPCPGPGP(MRG)PCPGPCPCPG)-3')	D [auth P], H [auth F]	21	Human immunodeficiency virus 1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	I [auth G], J [auth H]	2		N/A	Interactions Focus chain I [auth G] Focus chain J [auth H] Interactions & Density Focus chain I [auth G] Focus chain J [auth H]
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DDS Query on DDS Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain S [auth C] MOL2 format, chain M [auth A] MOL2 format, chain S [auth C]	M [auth A], S [auth C]	2',3'-dideoxyadenosine triphosphate C₁₀ H₁₆ N₅ O₁₁ P₃ OAKPWEUQDVLTCN-NKWVEPMBSA-N		Interactions Focus chain M [auth A] Focus chain S [auth C] Interactions & Density Focus chain M [auth A] Focus chain S [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B]	O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain R [auth T] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth T] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D]	N [auth A] P [auth B] Q [auth B] R [auth T] V [auth D] N [auth A], P [auth B], Q [auth B], R [auth T], V [auth D], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth T] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth T] Focus chain V [auth D] Focus chain W [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C]	K [auth A], L [auth A], T [auth C], U [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth C] Focus chain U [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
DDS	BindingDB: 5TXM	Ki: min: 20, max: 1200 (nM) from 4 assay(s)
DDS	BindingDB: 5TXM	IC50: 0.5 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	I [auth G], J [auth H]	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain I [auth G] Focus chain J [auth H] Interactions & Density Focus chain I [auth G] Focus chain J [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.223
R-Value Work: 0.184
R-Value Observed: 0.185
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.337	α = 90
b = 133.946	β = 97.71
c = 139.399	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Das, K.

Martinez, S.M.

Arnold, E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI027690

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 1.1: 2017-04-26
Changes: Database references
Version 1.2: 2017-06-07
Changes: Database references
Version 1.3: 2017-09-20
Changes: Author supporting evidence
Version 1.4: 2019-12-11
Changes: Author supporting evidence
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