BMRB Entry 4630

Name: NMR STRUCTURE OF THROMBOMODULIN EGF(4-5)
Published: 2001-05-07

Click here to enlarge.

PDB ID: 1dqb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR4630
MolProbity Validation Chart

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

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

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

NMR STRUCTURE OF THROMBOMODULIN EGF(4-5)

Deposition date:

2000-01-03

Original release date:

2001-05-07

Authors:

Wood, M.; Sampoli-Benitez, B.; Komives, E.

Citation:

Citation: Wood, M.; Sampoli-Benitez, B.; Komives, E.. "Solution structure of the smallest cofactor-active fragment of thrombomodulin" Nat. Struct. Biol. 7, 200-204 (2000).
PubMed: 10700277

Assembly members:

Assembly members:
THROMBOMODULIN, polymer, 83 residues, Formula weight is not available
NAG, non-polymer, 221.208 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: Pichia pastoris

Entity Sequences (FASTA):

Entity Sequences (FASTA):
THROMBOMODULIN: HMEPVDPCFRANCEYQCQPL NQTSYLCVCAEGFAPIPHEP HRCQMFCNQTACPADCDPNT QASCECPEGYILDDGFICTD IDE

Data sets:

coupling_constants
- JHNHA
- JHAHB

Data type	Count
coupling constants	43

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	THROMBOMODULIN	1
2	N-ACETYL-D-GLUCOSAMINE-1	2
3	N-ACETYL-D-GLUCOSAMINE-2	2

Entities:

Entity 1, THROMBOMODULIN 83 residues - Formula weight is not available

1

HIS

MET

GLU

PRO

VAL

ASP

PRO

CYS

PHE

ARG

2

ALA

ASN

CYS

GLU

TYR

GLN

CYS

GLN

PRO

LEU

3

ASN

GLN

THR

SER

TYR

LEU

CYS

VAL

CYS

ALA

4

GLU

GLY

PHE

ALA

PRO

ILE

PRO

HIS

GLU

PRO

5

HIS

ARG

CYS

GLN

MET

PHE

CYS

ASN

GLN

THR

6

ALA

CYS

PRO

ALA

ASP

CYS

ASP

PRO

ASN

THR

7

GLN

ALA

SER

CYS

GLU

CYS

PRO

GLU

GLY

TYR

8

ILE

LEU

ASP

GLY

PHE

ILE

CYS

THR

ASP

9

ILE

ASP

GLU

Entity 2, N-ACETYL-D-GLUCOSAMINE-1 - C8 H15 N O6 - 221.208 Da.

1

NAG

Samples:

sample_1: THROMBOMODULIN, [U-15N], 1 mM; N-ACETYL-D-GLUCOSAMINE 2 mM; H2O 90%; D2O 10%

sample_2: THROMBOMODULIN 1 mM; N-ACETYL-D-GLUCOSAMINE 2 mM; D2O 100%

sample_cond_1: pH: 6.5; temperature: 310 K; ionic strength: 0 M; pressure: 1 atm

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-separated NOESY	not available	not available	sample_cond_1
HNHA	not available	not available	sample_cond_1
2D NOESY	not available	not available	sample_cond_1

Software:

XWINNMR v3.0 - collection

FELIX v97.0 - data analysis

DGII v97.0 - structure solution

X-PLOR v3.5 - refinement

NMR spectrometers:

Bruker DRX 600 MHz

PDB	1DQB 1DX5 1ZAQ 3GIS
DBJ	BAA00149 BAG53913 BAJ17754
EMBL	CAA29045
GB	AAA61175 AAB27209 AAB59508 AAD49735 AAH35602
PRF	1403353A
REF	NP_000352 XP_003829427 XP_525283
SP	P07204 Q71U07
AlphaFold	P07204 Q71U07