Biological Assembly 1  

 3D View: Structure

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: 22.37 kDa 
• Atom Count: 1672 
• Modelled Residue Count: 205 
• Deposited Residue Count: 205 
• Unique protein chains: 2

7HVP

X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A COMPLEX BETWEEN A SYNTHETIC PROTEASE OF HUMAN IMMUNODEFICIENCY VIRUS 1 AND A SUBSTRATE-BASED HYDROXYETHYLAMINE INHIBITOR

• DOI: 10.2210/pdb7HVP/pdb

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


• Deposited: 1990-09-13 Released: 1993-07-15 
• Deposition Author(s): Swain, A.L., Miller, M.M., Green, J., Rich, D.H., Schneider, J., Kent, S.B.H., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Observed: 0.146 

Literature

X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor.

Swain, A.L., Miller, M.M., Green, J., Rich, D.H., Schneider, J., Kent, S.B., Wlodawer, A.

(1990) Proc Natl Acad Sci U S A 87: 8805-8809

• PubMed: 2247451 
• DOI: 10.1073/pnas.87.22.8805
• Primary Citation of Related Structures:  
  7HVP


• PubMed Abstract: 
  

The structure of a crystal complex of the chemically synthesized protease of human immunodeficiency virus 1 with a heptapeptide-derived inhibitor bound in the active site has been determined. The sequence of the inhibitor JG-365 is Ac-Ser-Leu-Asn-Phe-psi[CH(OH)CH2N]-Pro-Ile-Val-OMe; the Ki is 0.24 nM. The hydroxyethylamine moiety, in place of the normal scissile bond of the substrate, is believed to mimic a tetrahedral reaction intermediate. The structure of the complex has been refined to an R factor of 0.146 at 2.4-A resolution by using restrained least squares with rms deviations in bond lengths of 0.02 A and bond angles of 4. The bound inhibitor diastereomer has the S configuration at the hydroxyethylamine chiral carbon, and the hydroxyl group is positioned between the active site aspartate carboxyl groups within hydrogen bonding distance. Comparison of this structure with a reduced peptide bond inhibitor-protease complex indicates that these contacts confer the exceptional binding strength of JG-365.

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Related Citations: 

• Structure at 2.5-Angstroms Resolution of Chemically Synthesized Human Immunodeficiency Virus Type I Protease Complexed with a Hydroxyethylene-Based Inhibitor
  Jaskolski, M., Tomasselli, A.G., Sawyer, T.K., Staples, D.G., Heinrikson, R.L., Schneider, J., Kent, S.B., Wlodawer, A.
  (1991) Biochemistry 30: 1600

• Conserved Folding in Retroviral Proteases. Crystal Structure of a Synthetic HIV-1 Protease
  Wlodawer, A., Miller, M., Jaskolski, M., Sathyanarayana, B.K., Baldwin, E., Weber, I.T., Selk, L.M., Clawson, L., Schneider, J., Kent, S.B.H.
  (1989) Science 245: 616

• Structure of Complex of Synthetic HIV-1 Protease with a Substrate-Based Inhibitor at 2.3 Angstroms Resolution
  Miller, M., Schneider, J., Sathyanarayana, B.K., Toth, M.V., Marshall, G.R., Clawson, L., Selk, L., Kent, S.B.H., Wlodawer, A.
  (1989) Science 246: 1149

• Molecular Modeling of the HIV-1 Protease and its Substrate Binding Site
  Weber, I.T., Miller, M., Jaskolski, M., Leis, J., Skalka, A.M., Wlodawer, A.
  (1989) Science 243: 928

• Crystal Structure of a Retroviral Protease Proves Relationship to Aspartic Protease Family
  Miller, M., Jaskolski, M., Rao, J.K.M., Leis, J., Wlodawer, A.
  (1989) Nature 337: 576

• Enzymatic Activity of a Synthetic 99 Residue Protein Corresponding to the Putative HIV-1 Protease
  Schneider, J., Kent, S.B.H.
  (1988) Cell 54: 363

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Organizational Affiliation: 

Crystallography Laboratory, National Cancer Institute-Frederick Cancer Research and Development Center, MD 21702.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  EC: 3.4.23.16 (UniProt), 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 P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03369  Go to UniProtKB:  P03369

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INHIBITOR ACE-SER-LEU-ASN-PHE-PSI(CH(OH)-CH2N)-PRO-ILE VME (JG-365)	C	7	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	A, B	L-PEPTIDE LINKING	C4 H9 N O2		ALA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000228	C	JG-365	Peptide-like /  Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Observed: 0.146 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.2	α = 90
b = 58.8	β = 90
c = 62	γ = 90

Software Package:

Software Name	Purpose
PROFFT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1990-09-13 
• Released Date: 1993-07-15 
Deposition Author(s): Swain, A.L., Miller, M.M., Green, J., Rich, D.H., Schneider, J., Kent, S.B.H., Wlodawer, A.

Revision History  

• Version 1.0: 1993-07-15
  Type: Initial release
  
• Version 1.1: 2008-05-22
  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: 2013-02-27
  Changes: Other
• Version 1.4: 2014-08-06
  Changes: Derived calculations
• Version 1.5: 2017-11-29
  Changes: Derived calculations, Other