Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 22.39 kDa 
• Atom Count: 1799 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

1M0B

HIV-1 protease in complex with an ethyleneamine inhibitor

• DOI: 10.2210/pdb1M0B/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-06-12 Released: 2004-01-13 
• Deposition Author(s): Petrokova, H., Hasek, J., Dohnalek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.242 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Literature

Role of hydroxyl group and R/S configuration of isostere in binding properties of HIV-1 protease inhibitors

Petrokova, H., Duskova, J., Dohnalek, J., Skalova, T., Vondrackova-Buchtelova, E., Soucek, M., Konvalinka, J., Brynda, J., Fabry, M., Sedlacek, J., Hasek, J.

(2004) Eur J Biochem 271: 4451-4461

• PubMed: 15560786 
• DOI: 10.1111/j.1432-1033.2004.04384.x
• Primary Citation of Related Structures:  
  1M0B


• PubMed Abstract: 
  

The crystal structure of the complex between human immunodeficiency virus type 1 (HIV-1) protease and a peptidomimetic inhibitor of ethyleneamine type has been refined to R factor of 0.178 with diffraction limit 2.5 A. The peptidomimetic inhibitor Boc-Phe-Psi[CH2CH2NH]-Phe-Glu-Phe-NH2 (denoted here as OE) contains the ethyleneamine replacement of the scissile peptide bond. The inhibitor lacks the hydroxyl group which is believed to mimic tetrahedral transition state of proteolytic reaction and thus is suspected to be necessary for good properties of peptidomimetic HIV-1 protease inhibitors. Despite the missing hydroxyl group the inhibition constant of OE is 1.53 nm and it remains in the nanomolar range also towards several available mutants of HIV-1 protease. The inhibitor was found in the active site of protease in an extended conformation with a unique hydrogen bond pattern different from hydroxyethylene and hydroxyethylamine inhibitors. The isostere nitrogen forms a hydrogen bond to one catalytic aspartate only. The other aspartate forms two weak hydrogen bridges to the ethylene group of the isostere. A comparison with other inhibitors of this series containing isostere hydroxyl group in R or S configuration shows different ways of accommodation of inhibitor in the active site. Special attention is devoted to intermolecular contacts between neighbouring dimers responsible for mutual protein adhesion and for a special conformation of Met46 and Phe53 side chains not expected for free protein in water solution.

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Organizational Affiliation: 

Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Praha, Czech Republic. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE RETROPEPSIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0ZQ (Subject of Investigation/LOI)	C [auth B]	N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide C38 H49 N5 O7 CBWQRQVEXJTNOT-ZLESDFJESA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0ZQ	BindingDB:  1M0B	Ki: min: 1.5, max: 4.1 (nM) from 4 assay(s)
	Binding MOAD:  1M0B	Ki: 1.53 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000383 (0ZQ)	C [auth B]	BOC-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.242 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 6₁
• Diffraction Data DOI: 10.15785/SBGRID/730 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.7	α = 90
b = 62.7	β = 90
c = 82.23	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2002-06-12 
• Released Date: 2004-01-13 
Deposition Author(s): Petrokova, H., Hasek, J., Dohnalek, J.

Revision History  

• Version 1.0: 2004-01-13
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other