SMTL ID : 3unq.1

Bovine trypsin variant X(triplePhe227) in complex with small molecule inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 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 BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 12 residues within 4Å: Chain A: D.171, A.172, C.173, Q.174, S.177, V.191, W.193, G.194, G.196, C.197, G.204 Ligands: SO4.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.191 Hydrogen bonds: A:D.171, A:A.172, A:G.196 Water bridges: A:F.205

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

SO4.3: 4 residues within 4Å: Chain A: P.132, D.133, V.134, K.136 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.133, A:V.134 Water bridges: A:T.6, A:K.136, A:K.136 Salt bridges: A:K.136 SO4.9: 6 residues within 4Å: Chain A: H.40, Q.174, G.175, S.177 Ligands: BEN.2, PEG.8 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.174, A:G.175, A:S.177, A:S.177, A:S.177 Water bridges: A:F.24, A:S.177 Salt bridges: A:H.40

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: Q.115, C.116, L.117, K.139, V.182, C.183, S.184, G.185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.115, A:C.116, A:S.184, A:G.185 GOL.5: 2 residues within 4Å: Chain A: R.49 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.49, A:R.49 Water bridges: A:I.55 GOL.6: 4 residues within 4Å: Chain A: Y.5, C.7, T.11, L.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.7, A:T.11, A:K.139

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

EDO.7: 8 residues within 4Å: Chain A: N.19, G.21, Y.22, H.23, R.49, I.55, N.56 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.19, A:H.23, A:R.49

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 6 residues within 4Å: Chain A: F.24, H.40, C.41, Y.42, K.43 Ligands: SO4.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.40, A:Y.42

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

2012-11-21

Peptides

Cationic trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cationic trypsin

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