Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 44706.43 
• Atom Count: 3355 
• Residue Count: 398 
• Unique protein chains: 2

3K4V

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

• DOI: 10.2210/pdb3K4V/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 group M subtype B
• Expression System: Escherichia coli
• Mutation(s): 10 


• 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 

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: 10.1021/ml100046d


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
DMS	A, C, D	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ROC	B, 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 Fortovase; SAQUINAVIR,RO 31-8959 C38 H50 N6 O5 QWAXKHKRTORLEM-UGJKXSETSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000454 (ROC)	B,D	Saquinavir	Peptide-like / Inhibitor		--

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ARF	A, B	L-peptide NH3 amino terminus	C H3 N O		--

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ROC	IC50: 0.2 - 270 nM (93) BINDINGDB
ROC	Ki: 0 - 117 nM (100) BINDINGDB
ROC	Kd: 0.3 - 0.3 nM (93) BINDINGDB
ROC	ΔG: -35.5 - -62.3 kJ/mol (95) BINDINGDB
ROC	ΔH: 0.1 - 43.5 kJ/mol (96) BINDINGDB

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 51.205	α = 90.00
b = 62.673	β = 98.42
c = 59.076	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-06 
• 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
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2011-12-07
  Type: Database references
• Version 1.3: 2012-12-12
  Type: Other
• Version 1.4: 2014-09-24
  Type: Database references