BMRB Entry 16940

Name: Backbone 1H, 13C, 15N assignments for hirugen bound PPACKed thrombin
Published: 2010-07-26

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16940

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Backbone 1H, 13C, 15N assignments for hirugen bound PPACKed thrombin

Deposition date:

2010-05-20

Original release date:

2010-07-26

Authors:

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

Citation:

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).
PubMed: 20660315

Assembly members:

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:

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: pET23a

Entity Sequences (FASTA):

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:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	525
15N chemical shifts	253
1H chemical shifts	253

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Thrombin	1
2	Hirugen	2
3	PPACK	3
4	Sodium	4

Entities:

Entity 1, Thrombin 295 residues - 33810 Da.

Light and heavy chain of thrombin. Cleavage after R320

1

THR

PHE

GLY

SER

GLY

GLU

ALA

ASP

CYS

GLY

2

LEU

ARG

PRO

LEU

PHE

GLU

LYS

SER

LEU

3

GLU

ASP

LYS

THR

GLU

ARG

GLU

LEU

GLU

4

SER

TYR

ILE

ASP

GLY

ARG

ILE

VAL

GLU

GLY

5

SER

ASP

ALA

GLU

ILE

GLY

MET

SER

PRO

TRP

6

GLN

VAL

MET

LEU

PHE

ARG

LYS

SER

PRO

GLN

7

GLU

LEU

CYS

GLY

ALA

SER

LEU

ILE

SER

8

ASP

ARG

TRP

VAL

LEU

THR

ALA

HIS

CYS

9

LEU

TYR

PRO

TRP

ASP

LYS

ASN

PHE

10

THR

GLU

ASN

ASP

LEU

VAL

ARG

ILE

GLY

11

LYS

HIS

SER

ARG

THR

ARG

TYR

GLU

ARG

ASN

12

ILE

GLU

LYS

ILE

SER

MET

LEU

GLU

LYS

ILE

13

TYR

ILE

HIS

PRO

ARG

TYR

ASN

TRP

ARG

GLU

14

ASN

LEU

ASP

ARG

ASP

ILE

ALA

LEU

MET

LYS

15

LEU

LYS

PRO

VAL

ALA

PHE

SER

ASP

TYR

16

ILE

HIS

PRO

VAL

CYS

LEU

PRO

ASP

ARG

GLU

17

THR

ALA

SER

LEU

GLN

ALA

GLY

TYR

18

LYS

GLY

ARG

VAL

THR

GLY

TRP

GLY

ASN

LEU

19

LYS

GLU

THR

TRP

THR

ALA

ASN

VAL

GLY

LYS

20

GLY

GLN

PRO

SER

VAL

LEU

GLN

VAL

ASN

21

LEU

PRO

ILE

VAL

GLU

ARG

PRO

VAL

CYS

LYS

22

ASP

SER

THR

ARG

ILE

ARG

ILE

THR

ASP

ASN

23

MET

PHE

CYS

ALA

GLY

TYR

LYS

PRO

ASP

GLU

24

GLY

LYS

ARG

GLY

ASP

ALA

CYS

GLU

GLY

ASP

25

SER

GLY

PRO

PHE

VAL

MET

LYS

SER

PRO

26

PHE

ASN

ARG

TRP

TYR

GLN

MET

GLY

ILE

27

VAL

SER

TRP

GLY

GLU

GLY

CYS

ASP

ARG

ASP

28

GLY

LYS

TYR

GLY

PHE

TYR

THR

HIS

VAL

PHE

29

ARG

LEU

LYS

TRP

ILE

GLN

LYS

VAL

ILE

30

ASP

GLN

PHE

GLY

GLU

Entity 2, Hirugen 12 residues - 1468 Da.

C-terminal peptide of thrombin inhibitor Hirudin

1

GLY

ASP

PHE

GLU

ILE

PRO

GLU

TYR

2

LEU

GLN

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

1

PHE

PRO

ARG

CHM

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
3D TROSY HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D TROSY HNCACB	sample_1	isotropic	sample_conditions_1
3D TROSY HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CA)NNH	sample_1	isotropic	sample_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

UNP	P00734
AlphaFold	Q9UCA1