SMTL ID : 3v13.1

Bovine trypsin variant X(tripleGlu217Phe227) in complex with small molecule inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.52, N.54, V.57, E.62 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.52, A:N.54, A:V.57, H2O.1, H2O.1

1 x 3YH: 3-(3-carbamimidoylphenyl)-N-(2'-sulfamoylbiphenyl-4-yl)-1,2-oxazole-4-carboxamide(Non-covalent)

3YH.2: 18 residues within 4Å: Chain A: S.78, E.79, T.80, Y.81, F.154, I.155, D.171, A.172, C.173, Q.174, S.177, V.191, W.193, G.194, G.196, C.197, G.204 Ligands: SO4.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.154, A:V.191, A:W.193, A:W.193 Hydrogen bonds: A:D.171, A:D.171, A:Q.174, A:G.194 Water bridges: A:E.79, A:F.205 pi-Stacking: A:Y.81, A:F.154, A:F.154, A:W.193, A:W.193

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

SO4.3: 6 residues within 4Å: Chain A: H.40, Q.174, G.175, S.177 Ligands: 3YH.2, IMD.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.175, A:S.177, A:S.177 Salt bridges: A:H.40 SO4.4: 3 residues within 4Å: Chain A: Y.5, T.6 Ligands: GOL.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.6 Water bridges: A:T.6, A:T.6, A:T.6, A:K.136 Salt bridges: A:K.136 SO4.5: 1 residues within 4Å: Chain A: R.49 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.19, A:I.55 Salt bridges: A:R.49

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 4 residues within 4Å: Chain A: F.24, C.25, H.40 Ligands: SO4.3 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: I.1, V.2, G.3, G.4, Y.5, T.6, T.124, K.136 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.1, A:G.3, A:G.4, A:T.6 Water bridges: A:T.124

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: D.133, V.134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tziridis, A. et al., Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues. Biol.Chem. (2014)

Release Date

2012-12-12

Peptides

Cationic trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cationic trypsin

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