Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 22.31 kDa 
• Atom Count: 1646 
• Residue Count: 198 
• Unique protein chains: 1

1FQX

CRYSTAL STRUCTURE OF THE COMPLEX OF HIV-1 PROTEASE WITH A PEPTIDOMIMETIC INHIBITOR

• DOI: 10.2210/pdb1FQX/pdb

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


• Deposited: 2000-09-07 Released: 2001-03-14 
• Deposition Author(s): Dohnalek, J., Hasek, J., Duskova, J., Petrokova, H., Hradilek, M., Soucek, M., Konvalinka, J., Brynda, J., Sedlacek, J., Fabry, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Work: 0.180 
• R-Value Observed: 0.180 

Literature

A distinct binding mode of a hydroxyethylamine isostere inhibitor of HIV-1 protease.

Dohnalek, J., Hasek, J., Duskova, J., Petrokova, H., Hradilek, M., Soucek, M., Konvalinka, J., Brynda, J., Sedlacek, J., Fabry, M.

(2001) Acta Crystallogr D Biol Crystallogr 57: 472-476

• PubMed: 11223536 
• DOI: 10.1107/s0907444900018928
• Primary Citation of Related Structures:  
  1FQX


• PubMed Abstract: 
  

Crystallization conditions for an HIV-1 protease-inhibitor complex were optimized to produce crystals suitable for X-ray diffraction experiments. The X-ray structure of the HIV-1 protease complex was solved and refined at 3.1 A resolution. In contrast to Saquinavir, the mimetic hydroxy group of the inhibitor Boc-Phe-Psi[(S)-CH(OH)CH(2)NH]-Phe-Glu-Phe-NH(2) is placed asymmetrically with respect to the non-crystallographic twofold axis of the protease dimer so that hydrogen bonds between the amino group of the inhibitor and the catalytic aspartates can be formed. The inhibitor binds in the centre of the active site by a compact network of hydrogen bonds to Gly27, Gly127, Asp25, Asp125 and via the buried water molecule W301 to Ile50 and Ile150.

---

Organizational Affiliation: 

Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, 162 06 Praha 6, 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)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0ZT	A	N-{(2S,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide C38 H49 N5 O8 MPMUDVMRFYJRLP-XDIGFQIYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0ZT	Ki:  0.15000000596046448   nM  BindingDB
0ZT	Ki:  0.15000000596046448   nM  BindingDB
0ZT	Ki:  86   nM  BindingDB

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000386 (0ZT)	A	BOC-PHE-PSI[S-CH(OH)CH2NH]-PHE-GLU-PHE-NH2	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Work: 0.180 
• R-Value Observed: 0.180 
• Space Group: P 6₁
• Diffraction Data DOI: 10.15785/SBGRID/727 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.13	α = 90
b = 63.13	β = 90
c = 83.12	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-09-07 
• Released Date: 2001-03-14 
Deposition Author(s): Dohnalek, J., Hasek, J., Duskova, J., Petrokova, H., Hradilek, M., Soucek, M., Konvalinka, J., Brynda, J., Sedlacek, J., Fabry, M.

Revision History 

• Version 1.0: 2001-03-14
  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, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other