BMRB Entry 19305

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19305
MolProbity Validation Chart

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Title:
NMR structure of an inhibitor bound dengue NS3 protease
Deposition date:
2013-06-18
Original release date:
2014-07-07
Authors:
Gibbs, Al; Tounge, Brett; Steele, Ruth
Citation:

Citation: Gibbs, Al; Tounge, Brett; Steele, Ruth. "NMR structure of an inhibitor bound dengue NS3 protease provides new insights into the NS2B NS3 ligand interactions"  .

Assembly members:

Assembly members:
entity_1, polymer, 240 residues, 25785.062 Da.
ketobenzene, polymer, . residues, 120.154 Da.

Natural source:

Natural source:   Common Name: Dengue virus   Taxonomy ID: 12637   Superkingdom: Virus   Kingdom: not available   Genus/species: Flavivirus Dengue virus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSAADLELERAADVKWEDQA EISGSSPILSITISEDGSMS IKNEEEEQTLGGGGSGGGGE FAGVLWDVPSPPPVGKAELE DGAYRIKQKGILGYSQIGAG VYKEGTFHTMWHVTRGAVLM HKGKRIEPSWADVKKDLISY GGGWKLEGEWKEGEEVQVLA LEPGKNPRAVQTKPGLFKTN AGTIGAVSLDFSPGTSGSPI IDKKGKVVGLYGNGVVTRSG AYVSAIAQTEKSIEDNPEIE
ketobenzene: XXKRX

Data sets:
Data typeCount
13C chemical shifts712
15N chemical shifts217
1H chemical shifts537

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1dengue NS3 protease1
2ketobenzene2

Entities:

Entity 1, dengue NS3 protease 240 residues - 25785.062 Da.

1   GLYSERALAALAASPLEUGLULEUGLUARG
2   ALAALAASPVALLYSTRPGLUASPGLNALA
3   GLUILESERGLYSERSERPROILELEUSER
4   ILETHRILESERGLUASPGLYSERMETSER
5   ILELYSASNGLUGLUGLUGLUGLNTHRLEU
6   GLYGLYGLYGLYSERGLYGLYGLYGLYGLU
7   PHEALAGLYVALLEUTRPASPVALPROSER
8   PROPROPROVALGLYLYSALAGLULEUGLU
9   ASPGLYALATYRARGILELYSGLNLYSGLY
10   ILELEUGLYTYRSERGLNILEGLYALAGLY
11   VALTYRLYSGLUGLYTHRPHEHISTHRMET
12   TRPHISVALTHRARGGLYALAVALLEUMET
13   HISLYSGLYLYSARGILEGLUPROSERTRP
14   ALAASPVALLYSLYSASPLEUILESERTYR
15   GLYGLYGLYTRPLYSLEUGLUGLYGLUTRP
16   LYSGLUGLYGLUGLUVALGLNVALLEUALA
17   LEUGLUPROGLYLYSASNPROARGALAVAL
18   GLNTHRLYSPROGLYLEUPHELYSTHRASN
19   ALAGLYTHRILEGLYALAVALSERLEUASP
20   PHESERPROGLYTHRSERGLYSERPROILE
21   ILEASPLYSLYSGLYLYSVALVALGLYLEU
22   TYRGLYASNGLYVALVALTHRARGSERGLY
23   ALATYRVALSERALAILEALAGLNTHRGLU
24   LYSSERILEGLUASPASNPROGLUILEGLU

Entity 2, ketobenzene - 120.154 Da.

1   BEZNLELYSARGM9P

Samples:

sample_1: entity_1, [U-13C; U-15N; U-2H], 0.8 mM; entity_1, [U-5% 13C; U-100% 15N], 0.8 mM; entity_1, [U-13C; U-15N; U-2H]; [1H-13C]-I(delta1)LVM, 0.8 mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
3D CCH-NOESYsample_1isotropicsample_conditions_1
3D CNH-NOESYsample_1isotropicsample_conditions_1
3D NCH-NOESYsample_1isotropicsample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

X-PLOR, Brunger - structure solution

AutoStruct, Huang, Tejero, Powers and Montelione - structure solution

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

BMRB 18266 19080 19306
PDB
EMBL CAA40704
GB AIC36825 AIE47697 AIE47698 AIE47699 AIE47700
REF NP_739587
SP P27914
AlphaFold P27914

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