SMTL ID : 4mpx.1 (1 other biounit)

Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzothiene-4,2-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: W.14, H.108, T.205, W.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.206 Water bridges: A:W.206 SO4.2: 5 residues within 4Å: Chain A: H.44, Q.191, G.192, S.194 Ligands: 2AV.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.192, A:S.194, A:S.194 Salt bridges: A:H.44 SO4.6: 5 residues within 4Å: Chain B: H.44, Q.191, G.192, S.194 Ligands: 2AV.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.191, B:G.192, B:S.194, B:S.194 Salt bridges: B:H.44 SO4.7: 3 residues within 4Å: Chain B: H.156, R.173 Ligands: MES.11 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.156 Salt bridges: B:H.156, B:R.173 SO4.8: 3 residues within 4Å: Chain B: N.184, T.185, R.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.185, B:T.185 Salt bridges: B:R.186 SO4.12: 4 residues within 4Å: Chain C: W.14, H.108, T.205, W.206 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.206 Water bridges: C:W.206 SO4.13: 5 residues within 4Å: Chain C: H.44, Q.191, G.192, S.194 Ligands: 2AV.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.192, C:S.194, C:S.194 Salt bridges: C:H.44 SO4.17: 5 residues within 4Å: Chain D: H.44, Q.191, G.192, S.194 Ligands: 2AV.16 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.191, D:G.192, D:S.194, D:S.194 Salt bridges: D:H.44 SO4.18: 3 residues within 4Å: Chain D: H.156, R.173 Ligands: MES.22 3 PLIP interactions: 3 interactions with chain D Water bridges: D:H.156 Salt bridges: D:H.156, D:R.173 SO4.19: 3 residues within 4Å: Chain D: N.184, T.185, R.186 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.185, D:T.185 Salt bridges: D:R.186

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

CL.3: 4 residues within 4Å: Chain A: Q.5, V.148, K.149, R.187 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: E.154, N.155, R.229 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: Q.5, V.148, K.149, R.187 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain D: E.154, N.155, R.229 Ligand excluded by PLIP

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 6 residues within 4Å: Chain A: V.20, F.28, K.51, D.52, A.55, L.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.52 PGE.10: 6 residues within 4Å: Chain B: V.20, F.28, C.45, K.51, D.52, A.55 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.21 PGE.15: 6 residues within 4Å: Chain C: V.20, F.28, K.51, D.52, A.55, L.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.52 PGE.21: 6 residues within 4Å: Chain D: V.20, F.28, C.45, K.51, D.52, A.55 1 PLIP interactions: 1 interactions with chain D Water bridges: D:H.21

2 x 2AV: [(1,1,3,3-TETRAMETHYLDISILOXANE-1,3-DIYL)DI-1-BENZOTHIENE-4,2-DIYL]BIS({4-[3-(AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}METHANONE)(Non-covalent)

2AV.5: 30 residues within 4Å: Chain A: T.85, Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218, G.225 Chain B: T.85, Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218, G.225 Ligands: SO4.2, SO4.6 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.85, A:Q.87, A:Q.191, A:V.212, B:T.85, B:Q.87, B:Q.191, B:V.212 Hydrogen bonds: A:G.217, A:G.217, B:G.217, B:G.217 2AV.16: 30 residues within 4Å: Chain C: T.85, Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218, G.225 Chain D: T.85, Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218, G.225 Ligands: SO4.13, SO4.17 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:T.85, C:Q.87, C:Q.191, C:V.212, D:T.85, D:Q.87, D:Q.191, D:V.212 Hydrogen bonds: C:G.217, C:G.217, D:G.217, D:G.217

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.11: 4 residues within 4Å: Chain B: R.173, R.176, D.177 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.177, B:D.177 Salt bridges: B:R.176, B:D.177 MES.22: 4 residues within 4Å: Chain D: R.173, R.176, D.177 Ligands: SO4.18 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.177, D:D.177 Salt bridges: D:R.176, D:D.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giardina, S.F. et al., Target-directed self-assembly of homodimeric drugs. To be Published

Release Date

2015-03-18

Peptides

Tryptase alpha/beta-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Tryptase alpha/beta-1

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