SMTL ID : 6t0m.1

Cationic Trypsin in Complex with a D-Phe-Pro-diaminopyridine derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: R.72, I.78, N.79, V.80, V.81, F.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.72 DMS.2: 3 residues within 4Å: Chain A: N.100, S.101, N.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.101

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: E.75, D.76, N.77, I.78, V.80, V.81, E.82, E.85 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.75, A:N.77, A:V.80, A:E.85, H2O.1, H2O.3

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: P.129, T.130, S.131, S.207, K.209, Q.211 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.130, A:T.130, A:T.130, A:S.131, A:Q.211 Water bridges: A:K.209 Salt bridges: A:K.209

1 x GOZ: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[[2,6-bis(azanyl)pyridin-4-yl]methyl]pyrrolidine-2-carboxamide(Non-covalent)

GOZ.5: 16 residues within 4Å: Chain A: H.63, L.104, D.194, S.195, C.196, Q.197, S.200, V.214, S.215, W.216, G.217, S.218, G.219, G.227, V.228, Y.229 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.104, A:V.214 Hydrogen bonds: A:D.194, A:S.195, A:S.200, A:S.215, A:G.217, A:G.217, A:G.219, A:Y.229 Water bridges: A:S.218, A:S.218, A:V.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, K. et al., Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?. J.Med.Chem. (2020)

Release Date

2020-05-13

Peptides

Cationic trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cationic trypsin

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