3GI0 | pdb_00003gi0

Crystal structure of a chemically synthesized 203 amino acid 'covalent dimer' [l-ala51,d-ala51'] hiv-1 protease molecule complexed with jg-365 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3GI0/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Mutation(s): No 


• Deposited: 2009-03-04 Released: 2011-08-10 
• Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.237 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Correlations of protein dynamics with function in HIV-1 protease catalysis

Torbeev, V.Y., Kent, S.B.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 45.53 kDa 
• Atom Count: 3,308 
• Modeled Residue Count: 420 
• Deposited Residue Count: 420 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COVALENT DIMER [L-ALA51,D-ALA51'] HIV-1 PROTEASE	A, B	203	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
JG-365 inhibitor	C, D	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	A, B	L-PEPTIDE LINKING	C4 H9 N O2		ALA
DAL	A, B	D-PEPTIDE LINKING	C3 H7 N O2		--
NLE	A, B	L-PEPTIDE LINKING	C6 H13 N O2		LEU
YCM	A, B	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS
JG3	C, D	PEPTIDE-LIKE	C15 H22 N2 O3		--
VME	C, D	PEPTIDE-LIKE	C6 H13 N O2		--

Biologically Interesting Molecules (External Reference) 

1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.237 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.172	α = 90
b = 58.456	β = 90
c = 60.95	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Torbeev, V.Y., Kent, S.B.H.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Other
• Version 1.2: 2017-06-07
  Changes: Database references, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations