5XN1

HIV-1 reverse transcriptase Q151M:DNA:entecavir-triphosphate ternary complex

PDB DOI: https://doi.org/10.2210/pdb5XN1/pdb
NAKB: 5XN1

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

Deposited: 2017-05-17 Released: 2018-02-07
Deposition Author(s): Yasutake, Y., Tamura, N., Hayashi, H., Maeda, K.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.227
R-Value Work: 0.188
R-Value Observed: 0.190

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: 257.12 kDa
Atom Count: 17,562
Modelled Residue Count: 1,989
Deposited Residue Count: 2,078
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
Pol protein	A, D [auth C]	557	Human immunodeficiency virus 1	Mutation(s): 3 Gene Names: pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497 Go to UniProtKB: P12497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pol protein	B, E [auth D]	444	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497 Go to UniProtKB: P12497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
38-MER DNA aptamer	C [auth E], F	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	2		N/A	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ET9 Query on ET9 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain L [auth C]	H [auth A], L [auth C]	[[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate C₁₂ H₁₈ N₅ O₁₂ P₃ YMBBDUCQYPKKJK-FXQIFTODSA-N		Interactions Focus chain H [auth A] Focus chain L [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth F] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth F]	J [auth B], K [auth B], N [auth D], O [auth D], P [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth F] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C]	I [auth A], M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth C] Interactions & Density Focus chain I [auth A] Focus chain M [auth C]

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	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain G Interactions & Density Focus chain G

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.227
R-Value Work: 0.188
R-Value Observed: 0.190
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 284.707	α = 90
b = 284.707	β = 90
c = 95.793	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
MOLREP	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2018-02-07
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary