SMTL ID : 3pmj.2 (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

homo-dimer

Ligands

2 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 CA.9: 4 residues within 4Å: Chain B: E.52, N.54, V.57, E.62 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.52, B:N.54, B:V.57, B:E.62, H2O.17, H2O.18

2 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 PMJ.10: 17 residues within 4Å: Chain B: 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: SO4.15 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.81, B:Q.174, B:V.191 Hydrogen bonds: B:Y.81, B:A.172, B:S.177, B:S.192, B:G.194, B:G.196, B:G.196, B:Y.206 Water bridges: B:Y.81, B:S.195, B:I.205

2 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 GOL.11: 4 residues within 4Å: Chain B: V.58, E.62, Q.63, F.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.64, B:F.64

8 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: 4 residues within 4Å: Chain A: N.31, S.32, L.96 Chain B: K.186 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.32, A:S.32 Water bridges: A:S.102, B:K.186 Salt bridges: B:K.186 SO4.6: 5 residues within 4Å: Chain A: L.117, K.139 Chain B: N.97, S.98, R.99 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:Y.5, B:S.98, B:S.98, B:R.99 Water bridges: A:Y.5, A:Y.5, B:N.97, B:S.98, B:R.99, B:R.99, B:R.99 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 SO4.12: 3 residues within 4Å: Chain B: I.156, T.157, S.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.158 Water bridges: B:S.158 SO4.13: 4 residues within 4Å: Chain A: K.186 Chain B: N.31, S.32, L.96 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.32, B:S.32 Water bridges: B:S.102, A:K.186 Salt bridges: A:K.186 SO4.14: 5 residues within 4Å: Chain A: N.97, S.98, R.99 Chain B: L.117, K.139 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.98, A:S.98, A:R.99, B:Y.5, B:Y.5 Water bridges: A:N.97, A:S.98, A:S.98, A:R.99, A:R.99, A:R.99, B:K.139 Salt bridges: B:K.139 SO4.15: 5 residues within 4Å: Chain B: H.40, Q.174, G.175, S.177 Ligands: PMJ.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.174, B:G.175, B:S.177, B:S.177, B:S.177 Salt bridges: B:H.40

2 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 CL.16: 3 residues within 4Å: Chain B: 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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cationic trypsin

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