3IA9 | pdb_00003ia9

Crystal structure of a chemically synthesized [D25N]HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3IA9/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1
• Mutation(s): No 


• Deposited: 2009-07-13 Released: 2011-07-27 
• Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.208 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Hydrogen bonds at the protein-inhibitor interface in the HIV-1 protease / inhibitors complexes probed by total chemical synthesis and X-ray crystallography

Torbeev, V.Y., Kent, S.B.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.48 kDa 
• Atom Count: 1,794 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[D25N]HIV-1 protease	A, B	99	N/A	Mutation(s): 0  EC: 3.4.23.16
UniProt
Find proteins for O38732 (Human immunodeficiency virus type 1) Explore O38732  Go to UniProtKB:  O38732

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2NC	C [auth A]	N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide C35 H68 N11 O8 MQPXOVRKKPPKFZ-QYKDHROSSA-O
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	A, B	L-PEPTIDE LINKING	C4 H9 N O2		ALA
NLE	A, B	L-PEPTIDE LINKING	C6 H13 N O2		LEU
YCM	A, B	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000398 (2NC)	C [auth A]	N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.208 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.09	α = 90
b = 57.697	β = 90
c = 61.832	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Other
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary