SMTL ID : 5to3.1

Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- BMA- MAN- BMA- BMA- NAG- BMA: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-BMA-MAN-BMA-BMA-NAG-BMA.1: 2 residues within 4Å: Chain B: N.308, S.311 No protein-ligand interaction detected (PLIP)

1 x 0G6: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide(Covalent)

0G6.2: 19 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, S.205, S.226, A.227, G.228, G.230, C.231, G.238 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.179 Hydrogen bonds: B:A.200, B:E.202, B:G.203, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230 Water bridges: B:D.199, B:A.227, B:Y.240 Salt bridges: B:D.199

1 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain B: D.367, I.368, E.370, N.383, L.384, P.385, T.387 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.367, B:I.368, B:E.370, B:L.384, H2O.1

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain B: Y.190, R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.190 Water bridges: B:R.197, B:K.236

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 1 residues within 4Å: Chain B: N.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.53 NAG.6: 2 residues within 4Å: Chain B: F.333, N.335 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barranco-Medina, S. et al., Rational Design of Protein C Activators. Sci Rep (2017)

Release Date

2017-03-29

Peptides

Prothrombin: A
Prothrombin,Thrombomodulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prothrombin

Prothrombin,Thrombomodulin

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