3K4V

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

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


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

  • DOI: 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 co ...

    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.

    Organizational Affiliation: 

    Department of Chemical Sciences.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 ProteaseA, B100Human immunodeficiency virus type 1 BH10Mutation(s): 5 
Gene Names: gag-pol
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)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 ProteaseC, D99Human immunodeficiency virus type 1 BH10Mutation(s): 5 
Gene Names: gag-pol
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)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROC
Query on ROC
Download CCD File 
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
C38 H50 N6 O5
QWAXKHKRTORLEM-UGJKXSETSA-N		 Ligand Interaction
DMS
Query on DMS
Download CCD File 
A, C, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ROCKi:  0.20000000298023224   nM  BindingDB
ROCKd:  0.6399999856948853   nM  BindingDB
ROCKi:  0.41999998688697815   nM  BindingDB
ROCKi:  138   nM  BindingDB
ROCKd:  0.5799999833106995   nM  BindingDB
ROCIC50:  0.4000000059604645   nM  BindingDB
ROCKi:  0.03999999910593033   nM  BindingDB
ROCKi:  0.6499999761581421   nM  BindingDB
ROCIC50:  0.4000000059604645   nM  BindingDB
ROCKd:  4.099999904632568   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000454 (ROC)
Query on PRD_000454		B, DSaquinavirPeptide-like /  Inhibitor

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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 = 51.205α = 90
b = 62.673β = 98.42
c = 59.076γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

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