6KDJ
HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:lamivudine 5'-triphosphate ternary complex
- PDB DOI: https://doi.org/10.2210/pdb6KDJ/pdb
- NAKB: 6KDJ
- 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 
- Funding Organization(s): Japan Agency for Medical Research and Development (AMED)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.51 Å
- R-Value Free: 0.230 
- R-Value Work: 0.182 
- R-Value Observed: 0.184 
This is version 2.1 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 | A, D [auth C] | 557 | Human immunodeficiency virus 1 | Mutation(s): 5  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 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 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 AnnotationsExpand | |||||
|
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 AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
1RZ (Subject of Investigation/LOI) Query on 1RZ | H [auth A], L [auth C] | Lamivudine Triphosphate C8 H14 N3 O12 P3 S YLEQMGZZMCJKCN-NKWVEPMBSA-N | |||
GOL Query on GOL | J [auth B], K [auth B], N [auth D], O [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
MG Query on MG | I [auth A], M [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-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 | sucrose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.51 Å
- R-Value Free: 0.230 
- R-Value Work: 0.182 
- R-Value Observed: 0.184 
- Space Group: H 3
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 285.114 | α = 90 |
b = 285.114 | β = 90 |
c = 96.004 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-03-04  Deposition Author(s): Yasutake, Y., Hattori, S.I., Tamura, N., Maeda, K.
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