3K4V

New crystal form of HIV-1 Protease/Saquinavir structure reveals carbamylation of N-terminal proline

• PDB DOI: https://doi.org/10.2210/pdb3K4V/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-10-06 Released: 2010-06-09 
• Deposition Author(s): Olajuyigbe, F.M., Demitri, N., Ajele, J.O., Maurizio, E., Randaccio, L., Geremia, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.227 
• R-Value Observed: 0.159 

Literature

Carbamylation of N-terminal proline.

Olajuyigbe, F.M., Demitri, N., Ajele, J.O., Maurizio, E., Randaccio, L., Geremia, S.

(2010) ACS Med Chem Lett 1: 254-257

• PubMed: 24900204 
• DOI: https://doi.org/10.1021/ml100046d
• Primary Citation of Related Structures:  
  3K4V


• PubMed Abstract: 
  

  Protein carbamylation is of great concern both in vivo and in vitro. Here, we report the first structural characterization of a protein carbamylated at the N-terminal proline. The unexpected carbamylation of the α-amino group of the least reactive codified amino acid has been detected in high-resolution electron density maps of a new crystal form of the HIV-1 protease/saquinavir complex. The carbamyl group is found coplanar to the proline ring with a trans conformation. The reaction of N-terminal with cyanate ion derived from the chaotropic agent urea was confirmed by mass spectra analysis on protease single crystals. Implications of carbamylation process in vitro and in vivo are discussed.

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Organizational Affiliation: 

Department of Chemical Sciences ; Department of Biochemistry, Federal University of Technology, 340001 Akure, Nigeria.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.71 kDa 
• Atom Count: 3,547 
• Modelled Residue Count: 398 
• Deposited Residue Count: 398 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Protease	A, B	100	Human immunodeficiency virus type 1 BH10	Mutation(s): 5  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Protease	C, D	99	Human immunodeficiency virus type 1 BH10	Mutation(s): 5  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ROC	G [auth B], J [auth D]	(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide C38 H50 N6 O5 QWAXKHKRTORLEM-UGJKXSETSA-N
DMS	E [auth A], F [auth A], I [auth C], K [auth D]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
ROC	BindingDB:  3K4V	Ki: min: 0.04, max: 138 (nM) from 29 assay(s)
		Kd: min: 0.31, max: 67 (nM) from 6 assay(s)
		IC50: min: 0.2, max: 270 (nM) from 16 assay(s)
		-TΔS: min: -8.03e+1, max: -2.80e+1 (kJ/mol) from 47 assay(s)
		ΔH: min: -3.18e+1, max: 43.47 (kJ/mol) from 47 assay(s)
		ΔG: min: -6.23e+1, max: -3.55e+1 (kJ/mol) from 44 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000454 (ROC)	G [auth B], J [auth D]	Saquinavir	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.227 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.205	α = 90
b = 62.673	β = 98.42
c = 59.076	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
SHELXL-97	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Olajuyigbe, F.M., Demitri, N., Ajele, J.O., Maurizio, E., Randaccio, L., Geremia, S.

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2011-12-07
  Changes: Database references
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2014-09-24
  Changes: Database references
• Version 1.5: 2021-10-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-09-06
  Changes: Data collection, Refinement description