Biological Assembly 1  

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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: 22288.41 
• Atom Count: 1566 
• Residue Count: 198 
• Unique protein chains: 1

1FEJ

STRUCTURAL IMPLICATIONS OF DRUG RESISTANT MUTANTS OF HIV-1 PROTEASE: HIGH RESOLUTION CRYSTAL STRUCTURES OF THE MUTANT PROTEASE/SUBSTRATE ANALOG COMPLEXES

• DOI: 10.2210/pdb1FEJ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 group M subtype B
• Expression System: Escherichia coli
• Mutation(s): 6 


• Deposited: 2000-07-21 Released: 2001-06-01 
• Deposition Author(s): Mahalingam, B., Louis, J.M., Harrison, R.W., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.285 
• R-Value Work: 0.215 

Literature

Structural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes.

Mahalingam, B., Louis, J.M., Hung, J., Harrison, R.W., Weber, I.T.

(2001) Proteins 43: 455-464

• PubMed: 11340661 
• Primary Citation of Related Structures:  
  1FGC, 1FG8, 1FG6, 1FFI, 1FFF, 1FF0


• PubMed Abstract: 
  

Emergence of drug-resistant mutants of HIV-1 protease is an ongoing problem in the fight against AIDS. The mechanisms governing resistance are both complex and varied. We have determined crystal structures of HIV-1 protease mutants, D30N, K45I, N88D, and L90M complexed with peptide inhibitor analogues of CA-p2 and p2-NC cleavage sites in the Gag-pol precursor in order to study the structural mechanisms underlying resistance. The structures were determined at 1.55-1.9-A resolution and compared with the wild-type structure. The conformational disorder seen for most of the hydrophobic side-chains around the inhibitor binding site indicates flexibility of binding. Eight water molecules are conserved in all 9 structures; their location suggests that they are important for catalysis as well as structural stability. Structural differences among the mutants were analyzed in relation to the observed changes in protease activity and stability. Mutant L90M shows steric contacts with the catalytic Asp25 that could destabilize the catalytic loop at the dimer interface, leading to its observed decreased dimer stability and activity. Mutant K45I reduces the mobility of the flap and the inhibitor and contributes to an enhancement in structural stability and activity. The side-chain variations at residue 30 relative to wild-type are the largest in D30N and the changes are consistent with the altered activity observed with peptide substrates. Polar interactions in D30N are maintained, in agreement with the observed urea sensitivity. The side-chains of D30N and N88D are linked through a water molecule suggesting correlated changes at the two sites, as seen with clinical inhibitors. Structural changes seen in N88D are small; however, water molecules that mediate interactions between Asn88 and Thr74/Thr31/Asp30 in other complexes are missing in N88D.

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Organizational Affiliation: 

Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEASE RETROPEPSIN	C, D	99	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 6  Gene Names: gag-pol
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P04587

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
2NC	D	N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide p2/NC C35 H68 N11 O8 MQPXOVRKKPPKFZ-QYKDHROSSA-O

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000398 (2NC)	D	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: 1.78 Å
• R-Value Free: 0.285 
• R-Value Work: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 51.230	α = 90.00
b = 58.050	β = 90.00
c = 61.080	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
SCALEPACK	data scaling
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-07-21 
• Released Date: 2001-06-01 
• Deposition Author(s): Mahalingam, B., Louis, J.M., Harrison, R.W., Weber, I.T.

Revision History 

• Version 1.0: 2001-06-01
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2013-02-27
  Type: Other