BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 16940

Title: Backbone 1H, 13C, 15N assignments for hirugen bound PPACKed thrombin   PubMed: 20660315

Deposition date: 2010-05-20 Original release date: 2010-07-26

Authors: Lechtenberg, Bernhard; Johnson, Daniel; Freund, Stefan; Huntington, James

Citation: Lechtenberg, Bernhard; Johnson, Daniel; Freund, Stefan; Huntington, James. "NMR resonance assignments of thrombin reveal the conformational and dynamic effects of ligation."  Proc. Natl. Acad. Sci. U.S.A. 107, 14087-14092 (2010).

Assembly members:
Thrombin, polymer, 295 residues, 33810 Da.
Hirugen, polymer, 12 residues, 1468 Da.
PPACK, polymer, 4 residues, Formula weight is not available
NA, non-polymer, 22.990 Da.

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET23a

Entity Sequences (FASTA):
Thrombin: TFGSGEADCGLRPLFEKKSL EDKTERELLESYIDGRIVEG SDAEIGMSPWQVMLFRKSPQ ELLCGASLISDRWVLTAAHC LLYPPWDKNFTENDLLVRIG KHSRTRYERNIEKISMLEKI YIHPRYNWRENLDRDIALMK LKKPVAFSDYIHPVCLPDRE TAASLLQAGYKGRVTGWGNL KETWTANVGKGQPSVLQVVN LPIVERPVCKDSTRIRITDN MFCAGYKPDEGKRGDACEGD SGGPFVMKSPFNNRWYQMGI VSWGEGCDRDGKYGFYTHVF RLKKWIQKVIDQFGE
Hirugen: GDFEEIPEEYLQ
PPACK: FPRX

Data sets:
Data typeCount
13C chemical shifts525
15N chemical shifts253
1H chemical shifts253

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Thrombin1
2Hirugen2
3PPACK3
4Sodium4

Entities:

Entity 1, Thrombin 295 residues - 33810 Da.

Light and heavy chain of thrombin. Cleavage after R320

1   THRPHEGLYSERGLYGLUALAASPCYSGLY
2   LEUARGPROLEUPHEGLULYSLYSSERLEU
3   GLUASPLYSTHRGLUARGGLULEULEUGLU
4   SERTYRILEASPGLYARGILEVALGLUGLY
5   SERASPALAGLUILEGLYMETSERPROTRP
6   GLNVALMETLEUPHEARGLYSSERPROGLN
7   GLULEULEUCYSGLYALASERLEUILESER
8   ASPARGTRPVALLEUTHRALAALAHISCYS
9   LEULEUTYRPROPROTRPASPLYSASNPHE
10   THRGLUASNASPLEULEUVALARGILEGLY
11   LYSHISSERARGTHRARGTYRGLUARGASN
12   ILEGLULYSILESERMETLEUGLULYSILE
13   TYRILEHISPROARGTYRASNTRPARGGLU
14   ASNLEUASPARGASPILEALALEUMETLYS
15   LEULYSLYSPROVALALAPHESERASPTYR
16   ILEHISPROVALCYSLEUPROASPARGGLU
17   THRALAALASERLEULEUGLNALAGLYTYR
18   LYSGLYARGVALTHRGLYTRPGLYASNLEU
19   LYSGLUTHRTRPTHRALAASNVALGLYLYS
20   GLYGLNPROSERVALLEUGLNVALVALASN
21   LEUPROILEVALGLUARGPROVALCYSLYS
22   ASPSERTHRARGILEARGILETHRASPASN
23   METPHECYSALAGLYTYRLYSPROASPGLU
24   GLYLYSARGGLYASPALACYSGLUGLYASP
25   SERGLYGLYPROPHEVALMETLYSSERPRO
26   PHEASNASNARGTRPTYRGLNMETGLYILE
27   VALSERTRPGLYGLUGLYCYSASPARGASP
28   GLYLYSTYRGLYPHETYRTHRHISVALPHE
29   ARGLEULYSLYSTRPILEGLNLYSVALILE
30   ASPGLNPHEGLYGLU

Entity 2, Hirugen 12 residues - 1468 Da.

C-terminal peptide of thrombin inhibitor Hirudin

1   GLYASPPHEGLUGLUILEPROGLUGLUTYR
2   LEUGLN

Entity 3, PPACK 4 residues - Formula weight is not available

1   PHEPROARGCHM

Entity 4, Sodium - Na - 22.990 Da.

1   NA

Samples:

sample_1: Thrombin, [U-13C; U-15N; U-2H], 100 uM; Hirugen 110 uM; PPACK 100 uM; sodium phosphate 50 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 150 mM; pH: 7.4; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
3D TROSY HN(CO)CACBsample_1isotropicsample_conditions_1
3D TROSY HNCACBsample_1isotropicsample_conditions_1
3D TROSY HNCAsample_1isotropicsample_conditions_1
3D HN(CA)NNHsample_1isotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

SPARKY v3.110, Goddard - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Bruker Avance 900 MHz
  • Bruker Avance 800 MHz

Related Database Links:

UNP P00734
AlphaFold Q9UCA1

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