9DM9 | pdb_00009dm9

HIV-RT pre-catalytic complex with MK-8527

• PDB DOI: https://doi.org/10.2210/pdb9DM9/pdb
• NAKB: 9DM9

• Classification: TRANSFERASE/DNA
• Organism(s): HIV-1 M:B_HXB2R, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-09-12 Released: 2025-09-17 
• Deposition Author(s): Hayes, R.P., Tummala, S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.228 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Discovery of MK-8527, a novel long-acting nucleoside reverse transcriptase translocation inhibitor of HIV replication

Raheem, I., Girijavallabhan, V., Fillgrove, K., Goh, S., Bahnck-Teets, C., Huang, Q., Li, F., Wan, B., O'Donnell, G., Patteson, J., Cilento, M., Bennet, A., Bhardwaj, S., Hayes, R., Tummala, S., McHale, C., Wiltsie, J., Ellis, J., Asante-Appiah, E., Hazuda, D., Hale, J., Grobler, J., Carroll, S., Xu, M., Diamond, T., Lai, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 133.42 kDa 
• Atom Count: 8,622 
• Modeled Residue Count: 985 
• Deposited Residue Count: 1,065 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A	562	HIV-1 M:B_HXB2R	Mutation(s): 2  Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p51 RT	B	455	HIV-1 M:B_HXB2R	Mutation(s): 1  Gene Names: gag-pol
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA Primer	C [auth P]	21	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA Template	D [auth T]	27	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A6R (Subject of Investigation/LOI)	F [auth A]	2-chloro-7-{(4xi)-2-deoxy-4-ethynyl-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine C13 H16 Cl N4 O12 P3 NQMWULQTTWGPJA-IGJMFERPSA-N
MG	E [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.228 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.906	α = 90
b = 170.81	β = 90
c = 101.453	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Hayes, R.P., Tummala, S.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release