BMRB Entry 36532

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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/BMR36532
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
All files associated with the entry

Title:
Solution Structure of the C65A/C167A Mutant of Human Lipocalin-type Prostaglandin D Synthase
Deposition date:
2022-12-20
Original release date:
2025-11-04
Authors:
Miyamoto, Y.; Inui, T.
Citation:

Citation: Miyamoto, Yuya; Nakatsuji, Masatoshi; Yoshida, Takuya; Ohkubo, Tadayasu; Inui, Takashi. "Structural and interaction analysis of human lipocalin-type prostaglandin D synthase with the poorly water-soluble drug NBQX."  FEBS J. 290, 3983-3996 (2023).
PubMed: 37021622

Assembly members:

Assembly members:
Prostaglandin-H2 D-isomerase, polymer, 170 residues, 18796.988 Da.

Natural source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: not available   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Prostaglandin-H2 D-isomerase: GSAPEAQVSVQPNFQQDKFL GRWFSAGLASNSSWLREKKA ALSMAKSVVAPATDGGLNLT STFLRKNQCETRTMLLQPAG SLGSYSYRSPHWGSTYSVSV VETDYDQYALLYSQGSKGPG EDFRMATLYSRTQTPRAELK EKFTAFAKAQGFTEDTIVFL PQTDKCMTEQ

Data sets:
Data typeCount
13C chemical shifts662
15N chemical shifts170
1H chemical shifts975

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 170 residues - 18796.988 Da.

1   GLYSERALAPROGLUALAGLNVALSERVAL
2   GLNPROASNPHEGLNGLNASPLYSPHELEU
3   GLYARGTRPPHESERALAGLYLEUALASER
4   ASNSERSERTRPLEUARGGLULYSLYSALA
5   ALALEUSERMETALALYSSERVALVALALA
6   PROALATHRASPGLYGLYLEUASNLEUTHR
7   SERTHRPHELEUARGLYSASNGLNCYSGLU
8   THRARGTHRMETLEULEUGLNPROALAGLY
9   SERLEUGLYSERTYRSERTYRARGSERPRO
10   HISTRPGLYSERTHRTYRSERVALSERVAL
11   VALGLUTHRASPTYRASPGLNTYRALALEU
12   LEUTYRSERGLNGLYSERLYSGLYPROGLY
13   GLUASPPHEARGMETALATHRLEUTYRSER
14   ARGTHRGLNTHRPROARGALAGLULEULYS
15   GLULYSPHETHRALAPHEALALYSALAGLN
16   GLYPHETHRGLUASPTHRILEVALPHELEU
17   PROGLNTHRASPLYSCYSMETTHRGLUGLN

Samples:

sample_1: Prostaglandin-H2 D-isomerase, [U-13C; U-15N], 500 mM; acetic acid 20 mM; D2O, [U-2H], 10%; H2O 90%

sample_2: Prostaglandin-H2 D-isomerase, [U-13C; U-15N], 500 mM; acetic acid 20 mM; 99.95% D2O 100%

sample_conditions_1: ionic strength: 20 mM; pH: 4.0; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 20 mM; pH: 4.0; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
2D 13C-1H (HB)CB(CGCD)HDsample_2isotropicsample_conditions_2
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_2
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_2
3D HCCH-TOCSYsample_2isotropicsample_conditions_2
2D 1H-13C HSQCsample_2isotropicsample_conditions_2

Software:

Sparky v3.115, Goddard - chemical shift assignment

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

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMR spectrometers:

  • Varian INOVA 600 MHz

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