Biological Assembly 1  

 3D View: Structure | 1D-3D View | 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: 22.37 kDa 
• Atom Count: 1713 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

1B6L

HIV-1 PROTEASE COMPLEXED WITH MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 4

• PDB DOI: 10.2210/pdb1B6L/pdb

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


• Deposited: 1999-01-17 Released: 2000-01-07 
• Deposition Author(s): Martin, J.L., Begun, J., Schindeler, A., Wickramasinghe, W.A., Alewood, D., Alewood, P.F., Bergman, D.A., Brinkworth, R.I., Abbenante, G., March, D.R., Reid, R.C., Fairlie, D.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.226 
• R-Value Work: 0.202 

Literature

Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease.

Martin, J.L., Begun, J., Schindeler, A., Wickramasinghe, W.A., Alewood, D., Alewood, P.F., Bergman, D.A., Brinkworth, R.I., Abbenante, G., March, D.R., Reid, R.C., Fairlie, D.P.

(1999) Biochemistry 38: 7978-7988

• PubMed: 10387041 
• DOI: 10.1021/bi990174x
• Primary Citation of Related Structures:  
  1B6J, 1B6K, 1B6L, 1B6M, 1B6P, 1Z1H, 1Z1R


• PubMed Abstract: 
  

High-resolution crystal structures are described for seven macrocycles complexed with HIV-1 protease (HIVPR). The macrocycles possess two amides and an aromatic group within 15-17 membered rings designed to replace N- or C-terminal tripeptides from peptidic inhibitors of HIVPR. Appended to each macrocycle is a transition state isostere and either an acyclic peptide, nonpeptide, or another macrocycle. These cyclic analogues are potent inhibitors of HIVPR, and the crystal structures show them to be structural mimics of acyclic peptides, binding in the active site of HIVPR via the same interactions. Each macrocycle is restrained to adopt a beta-strand conformation which is preorganized for protease binding. An unusual feature of the binding of C-terminal macrocyclic inhibitors is the interaction between a positively charged secondary amine and a catalytic aspartate of HIVPR. A bicyclic inhibitor binds similarly through its secondary amine that lies between its component N-terminal and C-terminal macrocycles. In contrast, the corresponding tertiary amine of the N-terminal macrocycles does not interact with the catalytic aspartates. The amine-aspartate interaction induces a 1.5 A N-terminal translation of the inhibitors in the active site and is accompanied by weakened interactions with a water molecule that bridges the ligand to the enzyme, as well as static disorder in enzyme flap residues. This flexibility may facilitate peptide cleavage and product dissociation during catalysis. Proteases [Aba67,95]HIVPR and [Lys7,Ile33,Aba67,95]HIVPR used in this work were shown to have very similar crystal structures.

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Organizational Affiliation: 

Centre for Drug Design and Development, University of Queensland, Brisbane QLD 4072, Australia. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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 P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03369  Go to UniProtKB:  P03369

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PI4	E [auth A]	1-[2-(8-CARBAMOYLMETHYL-6,9-DIOXO-2-OXA-7,10-DIAZA-BICYCLO[11.2.2]HEPTADECA- 1(16),13(17),14-TRIEN-11-YL)-2-HYDROXY-ETHYL]-PIPERIDINE-2-CARBOXYLIC ACID TERT-BUTYLAMIDE C28 H43 N5 O6 GHEDXAXQQMZPLE-CWBXHPNXSA-N
SO4	C [auth A], D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Binding Affinity Annotations
ID	Source	Binding Affinity
PI4	PDBBind:  1B6L	Ki: 5 (nM) from 1 assay(s)
	Binding MOAD:  1B6L	Ki: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.226 
• R-Value Work: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.25	α = 90
b = 59.19	β = 90
c = 61.76	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-17 
• Released Date: 2000-01-07 
Deposition Author(s): Martin, J.L., Begun, J., Schindeler, A., Wickramasinghe, W.A., Alewood, D., Alewood, P.F., Bergman, D.A., Brinkworth, R.I., Abbenante, G., March, D.R., Reid, R.C., Fairlie, D.P.

Revision History  

• Version 1.0: 2000-01-07
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance