BMRB Entry 52100

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52100
MolProbity Validation Chart

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Title:
Solution NMR structure of Bcl-2-xL bound to compound 35
Deposition date:
2023-08-24
Original release date:
2023-08-28
Authors:
Pan, Yun-Zu; Rizo, Josep
Citation:

Citation: Pan, Yun-Zu; Liang, Qireng; Tomchick, Diana; de Brabander, Jef; Rizo, Josep. "Structural insights for selective disruption of Beclin 1 binding to Bcl-2"  Commun. Biol. 6, 1080-1080 (2023).
PubMed: 37875561

Assembly members:

Assembly members:
entity_1, polymer, 177 residues, Formula weight is not available
entity_2, non-polymer, 505 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-4T1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MAHAGRTGYDNREIVMKYIH YKLSQRGYEWDAGDDVEENR TEAPEGTESEVVHLTLRQAG DDFSRRYRRDFAEMSSQLHL TPFTARGRFATVVEELFRDG VNWGRIVAFFEFGGVMCVES VNREMSPLVDNIALWMTEYL NRHLHTWIQDNGGWDAFVEL YGPSMRPLFDFSWLSLK

Data sets:
Data typeCount
13C chemical shifts753
15N chemical shifts185
1H chemical shifts1194

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Bcl-2-xL1
2Compound 352

Entities:

Entity 1, Bcl-2-xL 177 residues - Formula weight is not available

1   METALAHISALAGLYARGTHRGLYTYRASP
2   ASNARGGLUILEVALMETLYSTYRILEHIS
3   TYRLYSLEUSERGLNARGGLYTYRGLUTRP
4   ASPALAGLYASPASPVALGLUGLUASNARG
5   THRGLUALAPROGLUGLYTHRGLUSERGLU
6   VALVALHISLEUTHRLEUARGGLNALAGLY
7   ASPASPPHESERARGARGTYRARGARGASP
8   PHEALAGLUMETSERSERGLNLEUHISLEU
9   THRPROPHETHRALAARGGLYARGPHEALA
10   THRVALVALGLUGLULEUPHEARGASPGLY
11   VALASNTRPGLYARGILEVALALAPHEPHE
12   GLUPHEGLYGLYVALMETCYSVALGLUSER
13   VALASNARGGLUMETSERPROLEUVALASP
14   ASNILEALALEUTRPMETTHRGLUTYRLEU
15   ASNARGHISLEUHISTHRTRPILEGLNASP
16   ASNGLYGLYTRPASPALAPHEVALGLULEU
17   TYRGLYPROSERMETARGPROLEUPHEASP
18   PHESERTRPLEUSERLEULYS

Entity 2, Compound 35 - C26 H24 Br N3 O3 - 505 Da.

Samples:

sample_1: Bcl-2-xL, [U-99% 13C; U-99% 15N], 300 ± 30 uM; Compound 35 300 ± 30 uM

sample_2: Bcl-2-xL, [U-99% 15N], 300 ± 30 uM; Compound 35 300 ± 30 uM

sample_3: Bcl-2-xL, [U-10% 13C], 100 ± 10 uM; Compound 35 100 ± 10 uM

sample_conditions_1: ionic strength: 0.0375 M; pH: 7.3; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D HBCBCGCDHDsample_1isotropicsample_conditions_1
2D HBCBCGCDCEHEsample_1isotropicsample_conditions_1
15N,13C-15N,13C-filtered homonuclear 2D TOCSYsample_1isotropicsample_conditions_1
15N,13C-15N,13C-filtered homonuclear 2D NOESYsample_1isotropicsample_conditions_1
simultaneous 3D 1H-15N, 1H-13C NOESY-HSQCsample_1isotropicsample_conditions_1
constant-time 1H-13C HSQCsample_1isotropicsample_conditions_1
constant-time 1H-13C HSQCsample_3isotropicsample_conditions_1

Software:

VNMRj v4.2 REVISION A - collection

NMRPipe v4.2 REVISION A - processing

VNMR v8.0.a15 - data analysis

CNS v1.2 - structure solution

NMR spectrometers:

  • Agilent DDX 800 MHz
  • Agilent DDX 600 MHz

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