1MTR | pdb_00001mtr

HIV-1 PROTEASE COMPLEXED WITH A CYCLIC PHE-ILE-VAL PEPTIDOMIMETIC INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb1MTR/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-02-15 Released: 1996-08-01 
• Deposition Author(s): Wickramasinghe, W., Begun, J., Martin, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.244 (Depositor) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Substrate-based cyclic peptidomimetics of Phe-Ile-Val that inhibit HIV-1 protease using a novel enzyme-binding mode.

March, D.R., Abbenante, G., Bergman, D.A., Brinkworth, R.I., Wickramasinghe, W., Begun, J., Martin, J.L., Fairlie, D.P.

(1996) J Am Chem Soc 118: 3375-3379

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 22.42 kDa 
• Atom Count: 1,718 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A, B	99	Human immunodeficiency virus 1	Mutation(s): 4  EC: 3.4.23.16
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
PI6	E [auth B]	[1-BENZYL-3-(8-SEC-BUTYL-7,10-DIOXO-2-OXA-6,9-DIAZA-BICYCLO[11.2.2] HEPTADECA-1(16),13(17),14-TRIEN-11-YLAMINO)-2-HYDROXY-PROPYL]-CARBAMIC ACID TERT-BUTYL ESTER C33 H48 N4 O6 RFUKEYSMPSCDLJ-CLFZCTPNSA-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

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000269 (PI6)	E [auth B]	tert-butyl [(1S,2S)-1-benzyl-2-hydroxy-3-{[(8S,11R)-8-[(1R)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9-diazabicyclo[11.2.2]heptadeca-1(15),13,16-trien-11-yl]amino}propyl]carbamate	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.244 (Depositor) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.4	α = 90
b = 58.7	β = 90
c = 62	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-08-01 
Deposition Author(s): Wickramasinghe, W., Begun, J., Martin, J.L.

Revision History  

• Version 1.0: 1996-08-01
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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: 2011-08-24
  Changes: Non-polymer description
• Version 1.4: 2012-07-25
  Changes: Non-polymer description
• Version 1.5: 2012-09-19
  Changes: Non-polymer description
• Version 1.6: 2012-12-12
  Changes: Other
• Version 1.7: 2021-11-03
  Changes: Database references, Derived calculations, Other
• Version 1.8: 2023-08-09
  Changes: Refinement description