6KDO

HIV-1 reverse transcriptase with Q151M/Y115F/F116Y/M184V/F160M:DNA:lamivudine 5'-triphosphate ternary complex

PDB DOI: https://doi.org/10.2210/pdb6KDO/pdb
NAKB: 6KDO

Classification: TRANSFERASE/DNA
Organism(s): Human immunodeficiency virus 1, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-07-02 Released: 2020-03-04
Deposition Author(s): Yasutake, Y., Hattori, S.I., Tamura, N., Maeda, K.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.230
R-Value Work: 0.192
R-Value Observed: 0.194

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: 256.87 kDa
Atom Count: 17,434
Modelled Residue Count: 1,989
Deposited Residue Count: 2,078
Unique protein chains: 2
Unique nucleic acid chains: 1

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, D [auth C]	557	Human immunodeficiency virus 1	Mutation(s): 7 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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 RT p51 subunit	B, E [auth D]	444	Human immunodeficiency virus 1	Mutation(s): 2
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
DNA/RNA (38-MER)	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1RZ (Subject of Investigation/LOI) Query on 1RZ Download Ideal Coordinates CCD File SDF format, chain J [auth E] SDF format, chain K [auth C] MOL2 format, chain J [auth E] MOL2 format, chain K [auth C]	J [auth E], K [auth C]	Lamivudine Triphosphate C₈ H₁₄ N₃ O₁₂ P₃ S YLEQMGZZMCJKCN-NKWVEPMBSA-N		Interactions Focus chain J [auth E] Focus chain K [auth C] Interactions & Density Focus chain J [auth E] Focus chain K [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D]	H [auth A], I [auth B], L [auth C], M [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
1RZ	BindingDB: 6KDO	Ki: 188 (nM) from 1 assay(s)
1RZ	BindingDB: 6KDO	Kd: 1.50e+4 (nM) from 1 assay(s)

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: 2.57 Å
R-Value Free: 0.230
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 284.239	α = 90
b = 284.239	β = 90
c = 95.948	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP19fk0310113

Revision History (Full details and data files)

Version 1.0: 2020-03-04
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