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

Human beta-tryptase co-crystal structure with {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: H.44, Q.191, G.192, S.194 Ligands: X00.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.191, A:G.192, A:S.194, A:S.194 Water bridges: A:H.44 Salt bridges: A:H.44 SO4.3: 7 residues within 4Å: Chain A: G.4, Q.5, W.126, Q.147, V.148, K.149, R.187 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.5, A:Q.147, A:Q.147, A:K.149 Salt bridges: A:R.187 SO4.5: 5 residues within 4Å: Chain B: H.44, Q.191, G.192, S.194 Ligands: X00.4 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 SO4.6: 2 residues within 4Å: Chain B: H.156, R.173 5 PLIP interactions: 5 interactions with chain B Water bridges: B:H.156, B:H.156, B:R.173 Salt bridges: B:H.156, B:R.173 SO4.7: 3 residues within 4Å: Chain B: N.184, T.185, R.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.185 Salt bridges: B:R.186 SO4.8: 5 residues within 4Å: Chain C: H.44, Q.191, G.192, S.194 Ligands: X00.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.191, C:G.192, C:S.194, C:S.194 Water bridges: C:H.44 Salt bridges: C:H.44 SO4.10: 7 residues within 4Å: Chain C: G.4, Q.5, W.126, Q.147, V.148, K.149, R.187 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.5, C:Q.147, C:Q.147, C:K.149 Salt bridges: C:R.187 SO4.12: 5 residues within 4Å: Chain D: H.44, Q.191, G.192, S.194 Ligands: X00.11 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 SO4.13: 2 residues within 4Å: Chain D: H.156, R.173 5 PLIP interactions: 5 interactions with chain D Water bridges: D:H.156, D:H.156, D:R.173 Salt bridges: D:H.156, D:R.173 SO4.14: 3 residues within 4Å: Chain D: N.184, T.185, R.186 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.185 Salt bridges: D:R.186

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 6 residues within 4Å: Chain A: V.20, F.28, C.45, K.51, D.52, A.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.50, A:D.52 PG4.9: 6 residues within 4Å: Chain C: V.20, F.28, C.45, K.51, D.52, A.55 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.50, C:D.52

2 x X00: {(1,1,3,3-TETRAMETHYLDISILOXANE-1,3-DIYL)BIS[5-(METHYLSULFANYL)BENZENE-3,1-DIYL]}BIS({4-[3-(AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}METHANONE)(Non-covalent)

X00.4: 29 residues within 4Å: Chain A: Y.84, Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218 Chain B: Y.84, 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: SO4.1, SO4.5 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.212, B:V.212 Hydrogen bonds: A:G.217, A:G.217, B:G.217, B:G.217 X00.11: 29 residues within 4Å: Chain C: Y.84, Q.87, D.188, S.189, C.190, Q.191, S.194, V.212, W.214, G.215, E.216, G.217, C.218 Chain D: Y.84, 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: SO4.8, SO4.12 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:V.212, C:V.212 Hydrogen bonds: D:G.217, D:G.217, C:G.217, C:G.217

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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