SMTL ID : 6ql0.1

Cationic Trypsin in Complex with a D-Phe-Pro-p-aminopyridine derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.1

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: R.72, I.78, N.79, V.80, V.81, F.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.72 Water bridges: A:N.42 EDO.3: 7 residues within 4Å: Chain A: C.132, A.133, I.165, F.184, Q.211, K.231 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.133, A:Q.211 EDO.4: 3 residues within 4Å: Chain A: V.81, E.85, F.87 No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain A: Q.197 Ligands: J5K.9 No protein-ligand interaction detected (PLIP) EDO.6: 8 residues within 4Å: Chain A: A.133, A.135, I.165, L.166, D.168, F.184, K.231 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.166, A:K.231

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

DMS.7: 5 residues within 4Å: Chain A: Y.28, C.30, T.34, V.35, L.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.28 DMS.8: 6 residues within 4Å: Chain A: C.233, N.234, Y.235, V.236, S.237, W.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.236, A:S.237, A:S.237

1 x J5K: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(6-azanylpyridin-3-yl)methyl]pyrrolidine-2-carboxamide(Non-covalent)

J5K.9: 17 residues within 4Å: Chain A: H.63, S.101, L.104, S.195, C.196, Q.197, S.200, V.214, S.215, W.216, G.217, G.219, C.220, G.227, V.228 Ligands: EDO.5, SO4.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.63, A:L.104, A:W.216 Hydrogen bonds: A:S.195 Water bridges: A:W.216, A:S.218, A:G.219

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

SO4.10: 5 residues within 4Å: Chain A: H.63, Q.197, G.198, S.200 Ligands: J5K.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.198, A:S.200, A:S.200 Salt bridges: A:H.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, K. et al., Thrombin in Complex with a D-Phe-Pro-diaminopyridine derivative. To Be Published

Release Date

2020-02-19

Peptides

Cationic trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cationic trypsin

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