BMRB Entry 4630
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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/BMR4630
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Title: NMR STRUCTURE OF THROMBOMODULIN EGF(4-5) PubMed: 10700277
Deposition date: 2000-01-03 Original release date: 2001-05-07
Authors: Wood, M.; Sampoli-Benitez, B.; Komives, E.
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).
Assembly members:
THROMBOMODULIN, polymer, 83 residues, Formula weight is not available
NAG, non-polymer, 221.208 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: Pichia pastoris
Entity Sequences (FASTA):
THROMBOMODULIN: HMEPVDPCFRANCEYQCQPL
NQTSYLCVCAEGFAPIPHEP
HRCQMFCNQTACPADCDPNT
QASCECPEGYILDDGFICTD
IDE
Additional metadata:
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 | 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