3HZC | pdb_00003hzc

Crystal structure of a chemically synthesized 203 amino acid 'covalent dimer' [Gly51;Aib51']HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3HZC/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)
• Mutation(s): No 


• Deposited: 2009-06-23 Released: 2011-04-27 
• Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.69 kDa 
• Atom Count: 1,729 
• Modeled Residue Count: 203 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Gly51;Aib51'] 'covalent dimer' HIV-1 protease	A	203	N/A	Mutation(s): 0  EC: 3.4.23.16
UniProt
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03369  Go to UniProtKB:  P03369

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2NC	B [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

Modified Residues  4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
AIB	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
NLE	A	L-PEPTIDE LINKING	C6 H13 N O2		LEU
YCM	A	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)	B [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: 1.45 Å
• R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.532	α = 90
b = 57.964	β = 90
c = 61.015	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: 2011-04-27 
Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2014-02-12
  Changes: Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection