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

Human beta-tryptase co-crystal structure with (2R,4S)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-4-hydroxy-2-(2-hydroxypropan-2-yl)-5,5-dimethyl-1,3-dioxolane-2,4-dicarboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

2 x 2A4: (2R,4S)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-4-hydroxy-2-(2-hydroxypropan-2-yl)-5,5-dimethyl-1,3-dioxolane-2,4-dicarboxamide(Non-covalent)

2A4.1: 27 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 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, G.225 Ligands: SO4.2, SO4.7 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.85, B:V.212, B:W.214, A:V.212 Hydrogen bonds: B:D.188, B:G.217, A:Q.87, A:Q.87, A:G.217, A:G.217 Water bridges: A:A.86 2A4.9: 27 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 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, G.225 Ligands: SO4.10, SO4.15 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:V.212, D:T.85, D:V.212, D:W.214 Hydrogen bonds: C:Q.87, C:Q.87, C:G.217, C:G.217, D:D.188, D:G.217 Water bridges: C:T.85, C:A.86

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

SO4.2: 5 residues within 4Å: Chain A: H.44, Q.191, G.192, S.194 Ligands: 2A4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.191, A:G.192, A:S.194, A:S.194 Salt bridges: A:H.44 SO4.4: 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 SO4.6: 3 residues within 4Å: Chain B: H.156, R.173 Ligands: MES.5 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.156 Salt bridges: B:H.156, B:R.173 SO4.7: 5 residues within 4Å: Chain B: H.44, Q.191, G.192, S.194 Ligands: 2A4.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.191, B:G.192, B:S.194 Salt bridges: B:H.44 SO4.10: 5 residues within 4Å: Chain C: H.44, Q.191, G.192, S.194 Ligands: 2A4.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.191, C:G.192, C:S.194, C:S.194 Salt bridges: C:H.44 SO4.12: 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 SO4.14: 3 residues within 4Å: Chain D: H.156, R.173 Ligands: MES.13 3 PLIP interactions: 3 interactions with chain D Water bridges: D:H.156 Salt bridges: D:H.156, D:R.173 SO4.15: 5 residues within 4Å: Chain D: H.44, Q.191, G.192, S.194 Ligands: 2A4.9 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.191, D:G.192, D:S.194 Salt bridges: D:H.44

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

MES.3: 7 residues within 4Å: Chain A: I.88, G.89, A.90, D.177, D.178, Y.232, Y.233 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.177, A:D.178, A:Y.232, A:Y.232 Water bridges: A:R.176, A:R.176 Salt bridges: A:D.178 MES.5: 4 residues within 4Å: Chain B: R.173, R.176, D.177 Ligands: SO4.6 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.11: 7 residues within 4Å: Chain C: I.88, G.89, A.90, D.177, D.178, Y.232, Y.233 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.177, C:D.178, C:Y.232 Water bridges: C:R.176, C:R.176 Salt bridges: C:D.178 MES.13: 4 residues within 4Å: Chain D: R.173, R.176, D.177 Ligands: SO4.14 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.177, D:D.177 Salt bridges: D:R.176, D:D.177

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

CL.8: 2 residues within 4Å: Chain B: N.155, R.229 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain D: N.155, R.229 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giardina, S.F. et al., Target-Directed Self-Assembly of Homodimeric Drugs Against beta-Tryptase. Acs Med.Chem.Lett. (2018)

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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