SMTL ID : 3pmj.1 (1 other biounit)

Bovine trypsin variant X(tripleIle227) in complex with small molecule inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 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 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.52, A:N.54, A:V.57, A:E.62, H2O.3, H2O.4

1 x PMJ: N~2~-(benzylsulfonyl)-D-arginyl-N-(4-carbamimidoylbenzyl)glycinamide(Non-covalent)

PMJ.2: 17 residues within 4Å: Chain A: H.40, E.79, Y.81, D.171, A.172, C.173, Q.174, S.177, V.191, S.192, W.193, G.194, S.195, G.196, C.197, G.204 Ligands: SO4.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.81, A:Q.174, A:V.191 Hydrogen bonds: A:Y.81, A:A.172, A:S.177, A:S.192, A:G.194, A:G.196, A:G.196, A:Y.206 Water bridges: A:S.195, A:I.205

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: V.58, E.62, Q.63, F.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.64, A:F.64

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

SO4.4: 3 residues within 4Å: Chain A: I.156, T.157, S.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.158 Water bridges: A:S.158 SO4.5: 3 residues within 4Å: Chain A: N.31, S.32, L.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.32, A:S.32 Water bridges: A:S.102 SO4.6: 2 residues within 4Å: Chain A: L.117, K.139 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.5 Water bridges: A:Y.5, A:Y.5 Salt bridges: A:K.139 SO4.7: 5 residues within 4Å: Chain A: H.40, Q.174, G.175, S.177 Ligands: PMJ.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.174, A:G.175, A:S.177, A:S.177, A:S.177 Salt bridges: A:H.40

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

CL.8: 3 residues within 4Å: Chain A: S.144, D.145, S.146 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

2011-11-23

Peptides

Cationic trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cationic trypsin

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