BMRB Entry 34225

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34225
MolProbity Validation Chart

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Title:
Solution structure of a last generation P2-P4 macrocyclic inhibitor
Deposition date:
2017-12-29
Original release date:
2019-01-28
Authors:
Gallo, M.; Eliseo, T.; Cicero, D.
Citation:

Citation: Gallo, M.; Eliseo, T.; Monteagudo, E.; Sabetta, S.; Paci, M.; Summa, V.; Cicero, D.. "Solution structure of a last generation macrocyclic inhibitor. Hepatitis C virus NS3 protease complex: when S prime region occupancy is not enough to stabilize the protein conformation in the absence of NS4A."  .

Assembly members:

Assembly members:
entity_1, polymer, 165 residues, 17444.971 Da.
entity_4P2, polymer, 5 residues, 775.953 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Hepacivirus C   Taxonomy ID: 31647   Superkingdom: Viruses   Kingdom: not available   Genus/species: Hepacivirus Hepacivirus C

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TGRDKNQVEGEVQVVSTATQ SFLATCVNGVCWTVYHGAGS KTLAGPKGPITQMYTNVDQD LVGWQAPPGARSLTPCTCGS SDLYLVTRHADVIPVRRRGD SRGSLLSPRPVSYLKGSSGG PLLCPSGHAVGIFRAAVCTR GVAKAVDFVPVESMETTMRA SKKKK
entity_4P2: XXXXX

Data sets:
Data typeCount
13C chemical shifts519
15N chemical shifts137
1H chemical shifts918

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3entity_33

Entities:

Entity 1, entity_1 165 residues - 17444.971 Da.

1   THRGLYARGASPLYSASNGLNVALGLUGLY
2   GLUVALGLNVALVALSERTHRALATHRGLN
3   SERPHELEUALATHRCYSVALASNGLYVAL
4   CYSTRPTHRVALTYRHISGLYALAGLYSER
5   LYSTHRLEUALAGLYPROLYSGLYPROILE
6   THRGLNMETTYRTHRASNVALASPGLNASP
7   LEUVALGLYTRPGLNALAPROPROGLYALA
8   ARGSERLEUTHRPROCYSTHRCYSGLYSER
9   SERASPLEUTYRLEUVALTHRARGHISALA
10   ASPVALILEPROVALARGARGARGGLYASP
11   SERARGGLYSERLEULEUSERPROARGPRO
12   VALSERTYRLEULYSGLYSERSERGLYGLY
13   PROLEULEUCYSPROSERGLYHISALAVAL
14   GLYILEPHEARGALAALAVALCYSTHRARG
15   GLYVALALALYSALAVALASPPHEVALPRO
16   VALGLUSERMETGLUTHRTHRMETARGALA
17   SERLYSLYSLYSLYS

Entity 2, entity_2 5 residues - 775.953 Da.

1   2KX2KYHYP0Y90YA

Entity 3, entity_3 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: HCV NS3 protease, [U-99% 15N], 500 uM; P2P4M, NA, 500 uM; sodium chloride, NA, 100 mM; n-octyl beta-D-glucopyranoside, deuterated, 0.3%; DTT, NA, 1 mM; sodium azide, NA, 0.01%

sample_2: HCV NS3 protease, [U-99% 15N] [U-99% 13C], 500 uM; P2P4M, NA, 500 uM; sodium chloride, NA, 100 mM; n-octyl beta-D-glucopyranoside, deuterated, 0.3%; DTT, NA, 1 mM; sodium azide, NA, 0.01%

sample_3: HCV NS3 protease, [U-99% 15N] [U-99% 13C], 500 uM; P2P4M, NA, 500 uM; sodium chloride, NA, 100 mM; n-octyl beta-D-glucopyranoside, deuterated, 0.3%; DTT, NA, 1 mM; sodium azide, NA, 0.01%

sample_conditions_1: ionic strength: 100 mM; pH: 6.8; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_3isotropicsample_conditions_1
3D CBCANHsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
F1-edited, F3-filtered 3D HMQC-NOESYsample_3isotropicsample_conditions_1
double-filtered [F1-C/N,F2-C/N]-NOESYsample_3isotropicsample_conditions_1

Software:

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

  • Bruker Avance 700 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks