1MUI | pdb_00001mui

Crystal structure of HIV-1 protease complexed with Lopinavir.

• PDB DOI: https://doi.org/10.2210/pdb1MUI/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-09-23 Released: 2002-10-23 
• Deposition Author(s): Stoll, V., Qin, W., Stewart, K.D., Jakob, C., Park, C., Walter, K., Simmer, R.L., Helfrich, R., Bussiere, D., Kao, J., Kempf, D., Sham, H.L., Norbeck, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.329 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.309 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystallographic Structure of ABT-378 (Lopinavir) Bound to HIV-1 Protease

Stoll, V., Qin, W., Stewart, K.D., Jakob, C., Park, C., Walter, K., Simmer, R.L., Helfrich, R., Bussiere, D., Kao, J., Kempf, D., Sham, H.L., Norbeck, D.W.

(2002) Bioorg Med Chem 10: 2803-2806

• PubMed: 12057670 
• DOI: https://doi.org/10.1016/s0968-0896(02)00051-2
• Primary Citation Related Structures: 
  1MUI


• PubMed Abstract: 
  

  The crystal structure of ABT-378 (lopinavir), bound to the active site of HIV-1 protease is described. A comparison with crystal structures of ritonavir, A-78791, and BILA-2450 shows some analogous features with previous reported compounds. A cyclic urea unit in the P(2) position of ABT-378 is novel and makes two bidentate hydrogen bonds with Asp 29 of HIV-1 protease. In addition, a previously unreported shift in the Gly 48 carbonyl position is observed. A discussion of the structural features responsible for its high potency against wild-type HIV protease is given along with an analysis of the effect of active site mutations on potency in in vitro assays.

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Organizational Affiliation: 
• Department of Structural Biology, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 22.24 kDa 
• Atom Count: 1,608 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protease	A [auth B], B [auth A]	99	Human immunodeficiency virus 1	Mutation(s): 1  EC: 3.4.23.16 (PDB Primary Data), 3.4.23.1 (UniProt)
UniProt
Find proteins for Q903J0 (Human immunodeficiency virus type 1) Explore Q903J0  Go to UniProtKB:  Q903J0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AB1	C [auth B]	N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE C37 H48 N4 O5 KJHKTHWMRKYKJE-SUGCFTRWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.329 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.309 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.264	α = 90
b = 63.264	β = 90
c = 83.621	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNX	refinement
HKL-2000	data reduction
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-23 
Deposition Author(s): Stoll, V., Qin, W., Stewart, K.D., Jakob, C., Park, C., Walter, K., Simmer, R.L., Helfrich, R., Bussiere, D., Kao, J., Kempf, D., Sham, H.L., Norbeck, D.W.

Revision History  

• Version 1.0: 2002-10-23
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Refinement description